Methods for Screening Bacteria, Archaea, Algae, and Yeast Using CRISPR Nucleic Acids

ABSTRACT

This invention relates to the use of CRISPR nucleic acids to screen for essential and non-essential genes and expendable genomic islands in bacteria, archaea, algae and/or yeast, to kill bacteria, archaea, algae and/or yeast, to identify the phenotype of a gene or genes, and/or to screen for reduced genome size and/or a gene deletion in bacteria, archaea, algae and/or yeast.

STATEMENT OF PRIORITY

This application is a continuation application of U.S. patent application Ser. No. 16/153,052, filed on Oct. 5, 2018, which is a continuation application of U.S. patent application Ser. No. 15/167,727, filed on May 27, 2016, now U.S. Pat. No. 10,136,649, issued on Nov. 27, 2018, which claims the benefit, under 35 U.S.C. § 119 (e), of U.S. Provisional Application No. 62/168,355 filed on May 29, 2015, and U.S. Provisional Application No. 62/296,853, filed on Feb. 18, 2016, the entire contents of each of which is incorporated by reference herein.

STATEMENT REGARDING ELECTRONIC FILING OF A SEQUENCE LISTING

A Sequence Listing in ASCII text format, submitted under 37 C.F.R. § 1.821, entitled 5051.881CT2.ST25.txt, 16,634 bytes in size, generated on Jan. 7, 2022, and filed via EFS-Web, is provided in lieu of a paper copy. This Sequence Listing is incorporated by reference into the specification for its disclosures.

FIELD OF THE INVENTION

The invention relates to the use of CRISPR nucleic acids to screen for essential and non-essential genes and expendable genomic islands in bacteria, archaea, algae and/or yeast, to kill bacteria, archaea, algae and/or yeast, to identify the phenotype of a gene or genes, and/or to screen for reduced genome size and/or a gene deletion in bacteria, archaea, algae and/or yeast.

BACKGROUND OF THE INVENTION

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), in combination with associated sequences (cas), constitute the CRISPR-Cas system, which confers adaptive immunity in many bacteria. CRISPR-mediated immunization occurs through the uptake of DNA from invasive genetic elements such as plasmids and phages, as novel “spacers.”

CRISPR-Cas systems consist of arrays of short DNA repeats interspaced by hypervariable sequences, flanked by cas genes, that provide adaptive immunity against invasive genetic elements such as phage and plasmids, through sequence-specific targeting and interference (Barrangou et al. 2007. Science. 315:1709-1712; Brouns et al. 2008. Science 321:960-4; Horvath and Barrangou. 2010. Science. 327:167-70; Marraffini and Sontheimer. 2008. Science. 322:1843-1845; Bhaya et al. 2011. Annu. Rev. Genet. 45:273-297; Terns and Terns. 2011. Curr. Opin. Microbiol. 14:321-327; Westra et al. 2012. Annu. Rev. Genet. 46:311-339; Barrangou R. 2013. RNA. 4:267-278). Typically, invasive DNA sequences are acquired as novel “spacers” (Barrangou et al. 2007. Science. 315:1709-1712), each paired with a CRISPR repeat and inserted as a novel repeat-spacer unit in the CRISPR locus. Subsequently, the repeat-spacer array is transcribed as a long pre-CRISPR RNA (pre-crRNA) (Brouns et al. 2008. Science 321:960-4), which is processed into small interfering CRISPR RNAs (crRNAs) that drive sequence-specific recognition. Specifically, crRNAs guide nucleases towards complementary targets for sequence-specific nucleic acid cleavage mediated by Cas endonucleases (Garneau et al. 2010. Nature. 468:67-71; Haurwitz et al. 2010. Science. 329:1355-1358; Sapranauskas et al. 2011. Nucleic Acid Res. 39:9275-9282; Jinek et al. 2012. Science. 337:816-821; Gasiunas et al. 2012. Proc. Natl. Acad. Sci. 109:E2579-E2586; Magadan et al. 2012. PLoS One. 7:e40913; Karvelis et al. 2013. RNA Biol. 10:841-851). These widespread systems occur in nearly half of bacteria (˜46%) and the large majority of archaea (˜90%).

In general terms, there are two main classes (Makarova et al. Nat Rev Microbiol. 13:722-736 (2015)) of CRISPR-Cas systems, which encompass five major types and 16 different subtypes based on cas gene content, cas operon architecture, Cas protein sequences, and process steps (Makarova et al. Biol Direct. 6:38 (2011); Makarova and Koonin Methods Mol Biol. 1311:47-75 (2015); Barrangou, R. Genome Biology 16:247 (2015)). In types I and III, the specialized Cas endonucleases process the pre-crRNAs, which then assemble into a large multi-Cas protein complex capable of recognizing and cleaving nucleic acids complementary to the crRNA. Type I systems are the most frequent and widespread systems, which target DNA in a Cascade-driven and PAM-dependent manner, destroying target nucleic acids by using the signature protein Cas3. A different process is involved in Type II CRISPR-Cas systems. Here, the pre-CRNAs are processed by a mechanism in which a trans-activating crRNA (tracrRNA) hybridizes to repeat regions of the crRNA. The hybridized crRNA-tracrRNA are cleaved by RNase III and following a second event that removes the 5′ end of each spacer, mature crRNAs are produced that remain associated with the both the tracrRNA and Cas9. The mature complex then locates a target dsDNA sequence (‘protospacer’ sequence) that is complementary to the spacer sequence in the complex and cuts both strands. Target recognition and cleavage by the complex in the type II system not only requires a sequence that is complementary between the spacer sequence on the crRNA-tracrRNA complex and the target ‘protospacer’ sequence but also requires a protospacer adjacent motif (PAM) sequence located at the 3′ end of the protospacer sequence.

SUMMARY OF THE INVENTION

One aspect of the invention provides a method of screening a population of bacterial cells for essential genes, non-essential genes, and/or expendable genomic islands, comprising: introducing into said population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial cells of said population, thereby producing a population of transformed bacterial cells; determining the presence or absence of a deletion in the population of transformed bacterial, archaeal, algal or yeast cells, wherein the presence of a deletion in the population of transformed bacterial, archaeal or yeast cells means that the target region is comprised within a non-essential gene and/or an expendable genomic island, and the absence of a deletion in the population of transformed bacterial, archaeal, algal or yeast cells means that the target region is comprised within an essential gene. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

A second aspect of the invention provides a method of screening a population of bacterial, archaeal, algal or yeast cells for essential genes, non-essential genes, and/or expendable genomic islands, comprising: introducing into the population of bacterial, archaeal, algal or yeast cells (a) a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (chromosomal and/or plasmid) of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, thereby producing a population of transformed bacterial, archaeal, algal or yeast cells; and determining the presence or absence of a deletion in the population of transformed bacterial, archaeal, algal or yeast cells, wherein the presence of a deletion in the population of transformed bacterial, archaeal or yeast cells means that the target region is comprised within a non-essential gene and/or an expendable genomic island, and the absence of a deletion in the population of transformed bacterial, archaeal, algal or yeast cells means that the target region is comprised within an essential gene.

A third aspect of the invention provides a method of killing one or more bacterial cells within a population of bacterial cells, comprising: introducing into the population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial cells of said population, thereby killing one or more bacterial cells that comprise the target region within the population of bacterial cells. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

A fourth aspect of the invention provides a method of killing one or more cells within a population of bacterial, archaeal, algal or yeast cells, comprising: introducing into the population of bacterial, archaeal, algal or yeast cells (a) a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (chromosomal and/or plasmid) of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, thereby killing one or more cells within a population of bacterial, archaeal, algal or yeast cells that comprise the target region in their genome.

A fifth aspect of the invention provides a method of identifying a phenotype associated with a bacterial gene, comprising: introducing into a population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of the at least one repeat-spacer sequence and repeat-spacer-repeat sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial cells of said population, wherein the target region comprises at least a portion of an open reading frame encoding a polypeptide or functional nucleic acid, thereby killing the cells comprising the target region and producing a population of transformed bacterial cells without the target region; and analyzing the phenotype of the population. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

A sixth aspect of the invention provides a method of identifying a phenotype of a bacterial, archaeal, algal or yeast gene, comprising: introducing into a population of bacterial, archaeal, algal or yeast cells (a) a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (chromosomal and/or plasmid) of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, thereby killing the bacterial, archaeal or yeast cells comprising the target region and producing a population of transformed bacterial, archaeal, algal or yeast cells without the target region; and analyzing the phenotype of the population of transformed bacterial, archaeal, algal or yeast cells, and/or (i) growing individual bacterial, archaeal, algal or yeast colonies from the population of transformed bacterial, archaeal, algal or yeast cells and (ii) analyzing the phenotype of the individual colonies.

A seventh aspect of the invention provides a method of selecting one or more bacterial cells having a reduced genome size from a population of bacterial cells, comprising: introducing into a population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population, wherein the cells comprising the target region are killed, thereby selecting one or more bacterial cells without the target region and having a reduced genome size from the population of bacterial cells. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

An eighth aspect of the invention provides a method of selecting one or more bacterial cells having a reduced genome size from a population of bacterial cells, comprising: introducing into a population of bacterial cells (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial cells or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and (b) a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population, wherein the target region is located between the one or more heterologous nucleic acid constructs introduced into the genome and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, and cells comprising the target region are killed, thereby selecting one or more bacterial cells without the target region and having a reduced genome size from the population of transgenic bacterial cells. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

A ninth aspect of the invention provides a method of selecting one or more bacterial, archaeal, algal or yeast cells having a reduced the genome size from a population of bacterial, archaeal, algal or yeast cells, comprising: introducing into a population of bacterial, archaeal, algal or yeast cells (a) a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of the at least one repeat-spacer sequence and the at least one repeat-spacer-repeat sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (chromosomal and/or plasmid) of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein cells comprising the target region are killed, thereby selecting one or more bacterial, archaeal, algal or yeast cells without the target region and having a reduced genome size from the population of bacterial, archaeal, algal or yeast cells.

A tenth aspect of the invention provides a method of selecting one or more bacterial, archaeal, algal or yeast cells having a reduced the genome size from a population of bacterial, archaeal or yeast cells, comprising: introducing into a population of bacterial, archaeal, algal or yeast cells: (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial, archaeal, algal or yeast cells, or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial, archaeal, algal or yeast cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and (b)(i) a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid, (ii) a heterologous nucleic acid construct comprising a CRISPR array comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of the at least one repeat-spacer sequence and the at least one repeat-spacer-repeat sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (chromosomal and/or plasmid) of one or more bacterial, archaeal, algal or yeast cells of said population, and (iii) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein the target region is located between the one or more heterologous nucleic acid constructs incorporated into the genome and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, and cells comprising the target region are killed, thereby selecting one or more bacterial, archaeal, algal or yeast cells without the target region and having a reduced genome size from the population of transgenic bacterial, archaeal, algal or yeast cells.

An eleventh aspect of the invention provides a method of identifying in a population of bacteria at least one isolate having a deletion in its genome, comprising: introducing into a population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population, wherein cells comprising the target region are killed, thereby producing a population of transformed bacterial cells without the target region; and growing individual bacterial colonies from the population of transformed bacterial cells, thereby identifying at least one isolate from the population of transformed bacteria having a deletion in its genome. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

A twelfth aspect of the invention provides a method of identifying in a population of bacteria at least one isolate having a deletion in its genome, comprising: introducing into the population of bacterial cells (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial cells or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and b) a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population, wherein the target region is located between the one or more heterologous nucleic acid constructs introduced into the genome and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, and cells comprising the target region are killed, thereby producing a population of transformed bacterial cells without the target region; and growing individual bacterial colonies from the population of transformed bacterial cells, thereby identifying at least one isolate from the population of bacteria having a deletion in its genome. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

A thirteenth aspect of the invention provides a method of identifying in a population of bacterial, archaeal, algal or yeast cells at least one isolate having a deletion in its genome, comprising: introducing into a population of bacterial, archaeal, algal or yeast cells: (a) a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (chromosomal and/or plasmid) of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein cells comprising the target region are killed, thereby producing a population of transformed bacterial, archaeal, algal or yeast cells without the target region; and growing individual bacterial, archaeal or yeast colonies from the population of transformed bacterial, archaeal, algal or yeast cells, thereby identifying at least one isolate from the population of transformed bacterial, archaeal, algal or yeast cells having a deletion in its genome.

A fourteenth aspect of the invention provides a method of identifying in a population of bacterial, archaeal, algal or yeast cells at least one isolate having a deletion in its genome, comprising: introducing into the population of bacterial, archaeal, algal or yeast cells (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial, archaeal, algal or yeast cells, or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial, archaeal, algal or yeast cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and (b)(i) a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid, (ii) a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (chromosomal and/or plasmid) of one or more bacterial, archaeal, algal or yeast cells of said population, and (iii) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein the target region is located between the one or more heterologous nucleic acid constructs incorporated into the genome and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, and cells comprising the target region are killed, thereby producing a population of transformed bacterial, archaeal, algal or yeast cells without the target region; and growing individual bacterial, archaeal or yeast colonies from the population of transformed bacterial, archaeal, algal or yeast cells, thereby identifying at least one isolate from the population having a deletion in its genome.

Further provided herein are expression cassettes, cells and kits comprising the nucleic acid constructs, nucleic acid arrays, nucleic acid molecules and/or nucleotide sequences of the invention.

These and other aspects of the invention are set forth in more detail in the description of the invention below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the sequence of SthCRISPR1 (SEQ ID NO:1) and SthCRISPR 3 arrays for targeting each composite transposon (LacZ (SEQ ID NO:2), ABC (SEQ ID NO:3), prtS (SEQ ID NO:4), cu (SEQ ID NO:5).

FIG. 2 shows a schematic of the splicing overlap extension (SOE) method for construction of targeting plasmids.

FIGS. 3A-3B show a map of essential genes, insertion sequences and genomic islands.

(A) The location and distribution of putative essential ORFs (top row), insertion sequences (2^(nd) row) and putative genomic islands (3^(rd) row). Potential targets for CRISPR-Cas (4^(th) row) mediated deletion were identified by mapping transposable elements of various families within the genome of Streptococcus thermophilus LMD-9. Genetic organization of putative genomic islands and the protospacer/PAM combinations corresponding to each. (B) provides four panels. The upper panel provides Genomic island 1, encoding an oligopeptide transport system (SEQ ID NO:6). The second panel from the top provides Genomic island 2, containing the cell-envelope proteinase PrtS (SEQ ID NO:7). The third panel from the top provides Genomic island 3, encoding an ATPase copper-efflux protein (SEQ ID NO:8) and the bottom panel provides the. (E) The genomic island encoding selected ORFs including the Lac operon (from left to right, SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11.

FIG. 4 provides a dendrogram of transposon coding sequences distributed throughout the genome of S. thermophilus LMD-9. The alignment was created using the Geneious® Software. Family designations were assigned using www-is.biotoul.fr. The letters A, B, C, and D correspond to alignments in FIG. 5 for each family.

FIG. 5A-5D show the alignments of transposon coding sequences (using Geneious® software) for each major IS family found in the S. thermophilus LMD-9 genome. Different families exhibited varying levels of conservation of length and nucleotide identity. (A) Sth6 transposons were highly polymorphic and apparently degenerate due to internal deletions in some of the copies. In contrast, IS1167 (B) and IS1191 (C) had fewer copies but maintained high fidelity in length and identity. IS1193 (D) had high fidelity copies but exhibited the greatest intra-family diversity in length.

FIG. 6A-6C show the structural basis for and apparent cytotoxicity of DNA targeting by CRISPR-Cas9. Spacer sequences for SthCRISPR1 (crRNA:SEQ ID NO:12; tracrRNA:SEQ ID NO:13; 5′ end of LacZ target DNA, upper strand: SEQ ID NO:15; lower strand: SEQ ID NO:14)(A) and SthCRISPR3 (crRNA:SEQ ID NO:16; tracrRNA:SEQ ID NO:17; 5′ end of LacZ target DNA, upper strand: SEQ ID NO:19; lower strand: SEQ ID NO:18) (B) for targeting lacZ. Cas9 interrogates DNA and binds reversibly to PAM sequences with stabilization of Cas9 at the target occurring via formation of the tracrRNA::crRNA duplex. Activation of the Cas9 causes simultaneous cleavage of each strand by the RuvC and HNH domains, as denoted by black wedges. Transformants recovered following electroporation of control and self-targeting plasmids (C). Average clones±SD screened across independent transformation experiments (n=4) for each of the plasmids tested.

FIGS. 7A-7B shows genome sequencing and phenotypic analysis of Lac⁻ clones. Sequence data revealed an absence of the chromosomal segment encoding lacZ in two mutants independently created by targeting the (A) 5′ end (upper panel) and cation-binding residue coding sequences of lacZ using the CRISPR3 system (lower panel). The size of the deletions ranged from 101,865-102,146 bp in length, constituting approximately 5.5% of the genome of S. thermophilus. (B) shows growth of large deletion strains compared to wild-type in semi-synthetic Elliker medium represented as mean±SD OD 600 nm of three independent biological replicates (upper panel) and acidification capacity of S. thermophilus strains in skim milk (lower panel).

FIG. 8 provides a depiction of recombination events between insertion sequences (IS). In the top left panel, a gel electrophoresis image of large deletion amplicons yielded by PCR analysis of gDNA recovered from transformants. Screening was performed using primers flanking the IS1193 elements upstream and downstream of the putative deletion site. Lanes denoted with A were amplified from gDNA of Lac⁻ clones recovered following CRISPR-Cas mediated targeting of lacZ, whereas WT is from wild-type. In the top middle panel, sequences of predicted recombination sites were determined by mapping single nucleotide polymorphisms corresponding to either upstream (SEQ ID NO:20) or downstream (SEQ ID NO:21) IS elements. The three sites are predicted based on sequences conserved in both IS elements. The sites depicted represent genotypes from independent clones and are representative of the Lac⁻ phenomenon observed at nine different recombination sites. Chimeric IS element footprints (SEQ ID NO:22) were similarly found in each genomic island locus at the deletion junction. The top right panel provides a schematic of IS's predicted to recombine during chromosomal deletion of the island encoding lacZ. The bottom left panel shows amplicons generated from primers flanking genomic islands 1, 2, and 3 to confirm deletions and the bottom right panel shows amplicons generated from internal primers to confirm the absence of wild-type sequences in each CRISPR-induced deletion culture. Lanes denoted with A were amplified from gDNA of clones recovered following CRISPR-Cas mediated targeting, and WT is wild-type.

FIG. 9 provides targets of lethality and shows use of defined genetic loci for assessing type II CRISPR-Cas system-based lethality via targeting the genome of Streptococcus thermophilus LMD-9. Both orthogonal type II systems (CRISPR1 and CRISPR3) were tested. Specific genetic features were selected to test (i) intergenic regions (INT), (ii) mobile genetic elements (ISSth7, oppC-GEI1, prtS-GEI2, copA-GEI3, cI, lacZ-GEI4, epsU), (iii) essential genes (dltA, ltaS), (iv) poles of the replichore (OriC, xerS), and forward vs. reverse strands of DNA (outer targets vs. inner targets).

FIG. 10 shows CRISPR-based lethality achieved by targeting the regions defined in FIG. 9. Log reduction in CFU (cell forming units) was calculated with regard to transformation of a non-targeting plasmid control; pORI28. Lethality ranged from 2-3 log reduction for all targets tested, regardless of chromosomal location, coding sequence, or essentiality. ISSth7-insertion sequence element, ltaS-lipoteichoic acid synthase; prtS-genomic island 2; INT-intergenic region; dltA-D-alanine ligase; rheB-chi site deficient locus; oppC-genomic island 1; comS-chi site dense locus; xerS-terminus of replication; copA-genomic island 3; cI-prophage remnant; OriC-origin of replication; Cas9-CRISPR3 Cas9 coding sequence; epsU-exopolysaccharide cassette.

FIG. 11 shows transcriptional profiles of CRISPR-mediated genomic island deletion strains.

FIG. 12 shows log₂ transformed RNA-sequencing read coverage of genomic island deletion strains, GEI1, GEI2, GEI3, and GEI4.

FIG. 13 shows XY plots of genomic island deletion strain expression values (X-axes) verses wild-type expression values (Y-axes). For each of the genomic island deletion strains (GEI1-GEI4), the expression of genes encoded on each of the target islands (black) was minimal. Genes encoded in GEI1 are shown in the top panel, genes encoded in GEI2 are shown in the second panel from the top, genes encoded in GEI3 are shown in the third panel from the top, and genes encoded in GEI4 are shown in the bottom panel.

FIG. 14A-14B shows introduction of an exogenous phage, plasmid or phagemid encoding CRISPR arrays (Type II system) to co-opt endogenous systems for programmed cell death in Streptococcus thermophiles. (A) CRISPR-Sth1 (crRNA:SEQ ID NO:12; tracrRNA:SEQ ID NO:13; 5′ end of LacZ target DNA, upper strand: SEQ ID NO:15; lower strand: SEQ ID NO:14) and (B) SthCRISPR3 (crRNA: SEQ ID NO:16; tracrRNA: SEQ ID NO:17; 5′ end of LacZ target DNA, upper strand: SEQ ID NO:19; lower strand: SEQ ID NO:18).

FIG. 15. The Type II guides of Lactobacillus casei. The first structure is the predicted guide (crRNA:SEQ ID NO:23; tracrRNA:SEQ ID NO:24; plasmid from L. vini, upper strand: SEQ ID NO:26; lower strand: SEQ ID NO:25). The second figure is the correct dual guide crRNA (SEQ ID NO:23):tracrRNA (SEQ ID NO:24) as confirmed by RNA Sequencing (plasmid from L. vini, upper strand: SEQ ID NO:26; lower strand: SEQ ID NO:25). The third figure is an example of a predicted artificial single guide (SEQ ID NO:28; plasmid from L. vini, upper strand: SEQ ID NO:26; lower strand: SEQ ID NO:25).

FIG. 16 provides exemplary Type II guides of Lactobacillus gasseri. The first structure is the predicted guide (crRNA: SEQ ID NO:29; tracrRNA: SEQ ID NO:30; protospacer: SEQ ID NO:31). The second figure is the correct dual guide crRNA (SEQ ID NO:29):tracrRNA (SEQ ID NO:32) as confirmed by RNA Sequencing. The third figure is an example of a predicted artificial single guide (SEQ ID NO:35; target DNA, upper strand: SEQ ID NO:37; lower strand: SEQ ID NO:36).

FIG. 17 provides exemplary Type II guides of Lactobacillus pentosus. The first structure is the predicted guide (crRNA:SEQ ID NO:38; tracrRNA:SEQ ID NO:39. The second figure is the correct dual guide crRNA (SEQ ID NO:38):tracrRNA (SEQ ID NO:40) as confirmed by RNA Sequencing. The third figure is an example of a predicted artificial single guide (SEQ ID NO:43; target DNA, upper strand: SEQ ID NO:42; lower strand: SEQ ID NO:41).

FIG. 18 provides exemplary Type II guides of Lactobacillus jensenii. The first figure is the correct dual guide crRNA (SEQ ID NO:44):tracrRNA (SEQ ID NO:45) as confirmed by RNA Sequencing (Lactobacillus phage LV-1, upper strand: SEQ ID NO:47, lower strand: SEQ ID NO:46). The bottom figure provides an example of a predicted artificial single guide (SEQ ID NO:48; Lactobacillus phage LV-1, upper strand: SEQ ID NO:47, lower strand: SEQ ID NO:46).

FIG. 19 shows the results of transformation of plasmids containing a protospacer that matches the most highly transcribe crRNA in the native L. gasseri Type II CRISPSR array. From left to right, four different plasmids were transformed into L. gasseri: an empty pTRK563 vector, a construct with the correct protospacer but an incorrect PAM, the correct PAM but a protospacer that is not in the array, and the correct protospacer with the PAM that demonstrated the most interference targeting and cell death. The reported values represent the mean±SEM of three independent replicates.

FIG. 20 shows transformation of plasmids containing a protospacer that matches the most highly transcribe crRNA in the native L. pentosus Type II CRISPSR array. From left to right, four different plasmids were transformed into L. pentosus: a construct with the correct protospacer but an incorrect PAM (Lpe4 ctGttt), the correct PAM but a protospacer that is not in the array (Lpe8 noSPCR), an empty pTRK563 vector (pTRK563), and a plasmid with the correct protospacer and correct PAM (Lpe1 gttaat). The reported values represent the mean±SEM of three independent replicates.

FIG. 21 provides an exemplary Type I CRISPR-Cas guide of Lactobacillus casei. The sequence provided is the native Type I leader (SEQ ID NO:49) and repeat that is found in Lactobacillus casei NCK 125. This artificial array contains a spacer that targets the 16s rDNA gene in the host genome. Repeat-spacer-repeat: SEQ ID NO:50.

FIG. 22 shows transformation of plasmids containing a protospacer that matches the most highly transcribe crRNA in the native L. jensenii Type II CRISPSR array. From left to right, four different plasmids were transformed into L. jensenii: an empty pTRK563 vector, a construct with the correct protospacer but an incorrect PAM, the correct PAM but a protospacer that is not in the array, and the correct protospacer with the PAM that demonstrated the most interference targeting and cell death.

FIG. 23 shows targeted self-killing using the native Type I system in Lactobacillus casei NCK 125. Two targets were designed in the 16s rDNA gene. The PAM 5′-YAA-3′ was predicted using the native spacer sequences in the organism. An artificial array containing the native Type I leader, repeats and the selected spacers was cloned into pTRK870. The constructs introduced included an empty vector (pTRK563) and two different artificial arrays: one containing a single spacer targeting the + strand in the 16s gene (1-2 alt) and the other array containing the original spacer targeting the + strand but containing an additional spacer targeting the − strand in the 16s gene (1, 2-3). The reported values represent the mean±SEM of three independent replicates.

DETAILED DESCRIPTION

The present invention now will be described hereinafter with reference to the accompanying drawings and examples, in which embodiments of the invention are shown. This description is not intended to be a detailed catalog of all the different ways in which the invention may be implemented, or all the features that may be added to the instant invention. For example, features illustrated with respect to one embodiment may be incorporated into other embodiments, and features illustrated with respect to a particular embodiment may be deleted from that embodiment. Thus, the invention contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. In addition, numerous variations and additions to the various embodiments suggested herein will be apparent to those skilled in the art in light of the instant disclosure, which do not depart from the instant invention. Hence, the following descriptions are intended to illustrate some particular embodiments of the invention, and not to exhaustively specify all permutations, combinations and variations thereof.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention.

All publications, patent applications, patents and other references cited herein are incorporated by reference in their entireties for the teachings relevant to the sentence and/or paragraph in which the reference is presented.

Unless the context indicates otherwise, it is specifically intended that the various features of the invention described herein can be used in any combination. Moreover, the present invention also contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. To illustrate, if the specification states that a composition comprises components A, B and C, it is specifically intended that any of A, B or C, or a combination thereof, can be omitted and disclaimed singularly or in any combination.

As used in the description of the invention and the appended claims, the singular forms “a,” “an” and “the” are intended to include the plural forms as well, unless the context clearly indicates otherwise.

Also as used herein, “and/or” refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (“or”).

The term “about,” as used herein when referring to a measurable value such as a dosage or time period and the like refers to variations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of the specified amount.

As used herein, phrases such as “between X and Y” and “between about X and Y” should be interpreted to include X and Y. As used herein, phrases such as “between about X and Y” mean “between about X and about Y” and phrases such as “from about X to Y” mean “from about X to about Y.”

The term “comprise,” “comprises” and “comprising” as used herein, specify the presence of the stated features, integers, steps, operations, elements, and/or components, but do not preclude the presence or addition of one or more other features, integers, steps, operations, elements, components, and/or groups thereof.

As used herein, the transitional phrase “consisting essentially of” means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim and those that do not materially affect the basic and novel characteristic(s) of the claimed invention. Thus, the term “consisting essentially of” when used in a claim of this invention is not intended to be interpreted to be equivalent to “comprising.”

“Cas9 nuclease” refers to a large group of endonucleases that catalyze the double stranded DNA cleavage in the CRISPR Cas system. These polypeptides are well known in the art and many of their structures (sequences) are characterized (See, e.g., WO2013/176772; WO/2013/188638). The domains for catalyzing the cleavage of the double stranded DNA are the RuvC domain and the HNH domain. The RuvC domain is responsible for nicking the (−) strand and the HNH domain is responsible for nicking the (+) strand (See, e.g., Gasiunas et al. PNAS 109(36):E2579-E2586 (Sep. 4, 2012)).

As used herein, “chimeric” refers to a nucleic acid molecule or a polypeptide in which at least two components are derived from different sources (e.g., different organisms, different coding regions).

“Complement” as used herein can mean 100% complementarity or identity with the comparator nucleotide sequence or it can mean less than 100% complementarity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like, complementarity).

The terms “complementary” or “complementarity,” as used herein, refer to the natural binding of polynucleotides under permissive salt and temperature conditions by base-pairing. For example, the sequence “A-G-T” binds to the complementary sequence “T-C-A.” Complementarity between two single-stranded molecules may be “partial,” in which only some of the nucleotides bind, or it may be complete when total complementarity exists between the single stranded molecules. The degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of hybridization between nucleic acid strands.

As used herein, “contact,” contacting,” “contacted,” and grammatical variations thereof, refers to placing the components of a desired reaction together under conditions suitable for carrying out the desired reaction (e.g., integration, transformation, screening, selecting, killing, identifying, amplifying, and the like). The methods and conditions for carrying out such reactions are well known in the art (See, e.g., Gasiunas et al. (2012) Proc. Natl. Acad. Sci. 109:E2579-E2586; M. R. Green and J. Sambrook (2012) Molecular Cloning: A Laboratory Manual. 4th Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).

A “deletion” as used herein can comprise the loss or deletion of genetic material including but not limited to a deletion of a portion of a chromosome or a plasmid, a deletion of a gene or a portion of a gene from a chromosome or a plasmid. In some embodiments, a deletion can comprise one gene or more than one gene. In some embodiments, a deletion may also comprise the loss of non-protein-coding regions that may encode small non-coding RNAs. In some embodiments, a deletion can comprise the loss of an entire plasmid or of an entire mobile genetic element. In some embodiments, the loss of a mobile genetic element may be defined as, for example, an inability to replicate or persist.

In some embodiments, a phasmid of the invention may comprise a CRISPR array from a Type I CRISPR-Cas system, a Type II CRISPR-Cas system, a Type III CRISPR-Cas system, a Type IV CRISPR-Cas system, and/or a Type V CRISPR-Cas system (see, Makarova et al. Nature Reviews Biotechnology 13:722736 (2015)).

Thus, in some embodiments, in addition to a Type I crRNA, a phasmid of the invention may comprise Type I polypeptides and/or Type I Cascade polypeptides (i.e., a Type I CRISPR-Cas system).

As used herein, “Type I polypeptide” refers to any of a Cas3 polypeptide, Cas3′ polypeptide, a Cas3″ polypeptide, fusion variants thereof, and any one or more of the Type I Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated complex for antiviral defense (“Cascade”) polypeptides. Thus, the term “Type I polypeptide” refers to the polypeptides that make up a Type I-A CRISPR-Cas system, a Type I-B CRISPR-Cas system, a Type I-C CRISPR-Cas system, a Type I-D CRISPR-Cas system, a Type I-E CRISPR-Cas system, a Type I-F CRISPR-Cas system, and/or a Type I-U CRISPR-Cas system. Each Type-I CRISPR-Cas system comprises at least one Cas3 polypeptide. Cas3 polypeptides generally comprise both a helicase domain and an HD domain. However, in some Type I CRISPR-Cas systems, the helicase and HD domain are found in separate polypeptides, Cas3′ and Cas3″. In particular, Cas3′ encodes the helicase domain whereas Cas3″ encodes the HD domain. Consequently, because both domains are required for Cas3 function, Type I subtypes either encode Cas3 (I-C, I-D, I-E, I-F, I-U) or Cas3′ and Cas3″ (I-A, I-B).

As used herein, “Type I Cascade polypeptides” refers to a complex of polypeptides involved in processing of pre-crRNAs and subsequent binding to the target DNA in Type I CRISPR-Cas systems. These polypeptides include, but are not limited to, the Cascade polypeptides of Type I subtypes I-A, I-B, I-C, I-D, I-E and I-F. Non-limiting examples of Type I-A Cascade polypeptides include Cas7 (Csa2), Cas8a1 (Csx13), Cas8a2 (Csx9), Cas5, Csa5, Cas6a, Cas3′ and/or a Cas3″. Non-limiting examples of Type I-B Cascade polypeptides include Cas6b, Cas8b (Csh1), Cas7 (Csh2) and/or Cas5. Non-limiting examples of Type I-C Cascade polypeptides include Cas5d, Cas8c (Csd1), and/or Cas7 (Csd2). Non-limiting examples of Type I-D Cascade polypeptides include Cas10d (Csc3), Csc2, Csc1, and/or Cas6d. Non-limiting examples of Type I-E Cascade polypeptides include Cse1 (CasA), Cse2 (CasB), Cas7 (CasC), Cas5 (CasD) and/or Cas6e (CasE). Non-limiting examples of Type I-F Cascade polypeptides include Cys1, Cys2, Cas7 (Cys3) and/or Cas6f (Csy4). Non-limiting examples of Type I-U Cascade polypeptides include Cas8c, Cas7, Cas5, Cas6 and/or Cas4.

In some embodiments, a phasmid of the invention may comprise may comprise a Type II CRISPR-Cas system in addition to a Type II crRNA. Type II CRISPR-Cas systems comprise three subtypes: Type II-A, Type II-B and Type II-C, each of which comprise the multidomain protein, Cas9, in addition to the adaptation polypeptides, Cas1, Cas2 and optionally, Csn2 and/or Cas4. Most Type II loci also encode a tracrRNA. Organisms comprising exemplary Type II CRISPR-Cas systems include Legionella pneumophila str. Paris, Streptococcus thermophilus CNRZ1066 and Neisseria lactamica 020-06.

In additional embodiments, a phasmid of the invention may comprise may comprise a Type III CRISPR-Cas system in addition to a Type III crRNA. Similar to Type I CRISPR-Cas systems, in Type III systems processing and interference is mediated by multiprotein CRISPR RNA (crRNA)-effector complexes (Makarova et al. Nature Reviews Biotechnology 13:722736 (2015))—“CASCADE” in Type I and “Csm” or “Cmr” in Type III. Thus, in some embodiments, a Type III CRISPR-Cas system can comprise a Csm complex (e.g., Type III-A Csm) and/or a Cmr complex (e.g., Type III-B Cmr), and optionally a Cas6 polypeptide. In representative embodiments, a Csm complex may comprise Cas10 (or Csm1), Csm2, Csm3, Csm4, Csm5, and Csm6 polypeptides and a Cmr complex may comprise Cmr1, Cas10 (or Cmr2), Cmr3, Cmr4, Cmr5, and Cmr6 polypeptides. In addition to the Csm complex or Cmr complex, a Type III CRISPR-Cas system may further comprise a Cas7 polypeptide. Four subtypes of a Type III CRISPR-Cas system have been characterized, III-A, III-B, III-D. In some embodiments, a Type III-A CRISPR-Cas system comprises Cas6, Cas10, Csm2, Cas7 (Csm3), Cas5 (Csm4), Cas7 (Csm5), and Csm6 polypeptides. In some embodiments, a Type III-B CRISPR-Cas system comprises Cas7 (Cmr1), Cas10, Cas5 (Cmr3), Cas7 (Cmr4), Cmr5, Cas6, and Cas7 (Cmr6) polypeptides. In some embodiments, a Type III-C CRISPR-Cas system comprises Cas7 (Cmr1), Cas7 (Cmr6), Cas10, Cas7 (Cmr4), Cmr5 and Cas5 (Cmr3), polypeptides. In some embodiments, a Type III-D CRISPR-Cas system comprises Cas10, Cas7 (Csm3), Cas5 (Csx10), Csm2, Cas7 (Csm3), and all1473 polypeptides.

In some embodiments, a phasmid of the invention may comprise a Type IV CRISPR-Cas system, in addition to a Type IV crRNA. Type IV CRISPR-Cas systems can comprise a Csf4 polypeptide (dinG) and/or a Csf1, Cas7 (Csf2) and/or Cas5 (csf3) polypeptide. (Makarova et al. Nature Reviews Microbiology 13:722-736 (2015)).

In some embodiments, a phasmid of the invention further comprises a Type V CRISPR-Cas system, in addition to a Type V crRNA. Type V CRISPR-Cas systems can comprise a Cpf1 polypeptide and/or a Cas1, Cas2 and/or Cas4 polypeptide. (Makarova et al. Nature Reviews Microbiology 13:722-736 (2015)).

A “fragment” or “portion” of a nucleotide sequence of the invention will be understood to mean a nucleotide sequence of reduced length relative (e.g., reduced by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more nucleotides) to a reference nucleic acid or nucleotide sequence and comprising, consisting essentially of and/or consisting of a nucleotide sequence of contiguous nucleotides identical or substantially identical (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identical) to the reference nucleic acid or nucleotide sequence. Such a nucleic acid fragment or portion according to the invention may be, where appropriate, included in a larger polynucleotide of which it is a constituent. Thus, hybridizing to (or hybridizes to, and other grammatical variations thereof), for example, at least a portion of a target DNA (e.g., target region in the genome), refers to hybridization to a nucleotide sequence that is identical or substantially identical to a length of contiguous nucleotides of the target DNA. In some embodiments, a repeat of a repeat spacer sequence or a repeat-spacer-repeat sequence can comprise a fragment of a repeat sequence of a wild-type CRISPR locus or a repeat sequence of a synthetic CRISPR array, wherein the fragment of the repeat retains the function of a repeat in a CRISPR array of hybridizing with the tracr nucleic acid.

In some embodiments, the invention may comprise a functional fragment of a Cas9, Cas3, Cas3′, Cas3″, or Cpf1 nuclease. A Cas9 functional fragment retains one or more of the activities of a native Cas9 nuclease including, but not limited to, HNH nuclease activity, RuvC nuclease activity, DNA, RNA and/or PAM recognition and binding activities. A functional fragment of a Cas9 nuclease may be encoded by a fragment of a Cas9 polynucleotide. A Cas3, Cas3′ or Cas3″ functional fragment retains one or more of the activities of a native Cas9 nuclease including, but not limited to, nickase activity, exonuclease activity, DNA-binding, and/or RNA binding. A functional fragment of a Cas3, Cas3′ or Cas3″ nuclease may be encoded by a fragment of a Cas3, Cas3′ or Cas3″ polynucleotide, respectively.

As used herein, the term “gene” refers to a nucleic acid molecule capable of being used to produce mRNA, antisense RNA, RNAi (miRNA, siRNA, shRNA), anti-microRNA antisense oligodeoxyribonucleotide (AMO), and the like. Genes may or may not be capable of being used to produce a functional protein or gene product. Genes can include both coding and non-coding regions (e.g., introns, regulatory elements, promoters, enhancers, termination sequences and/or 5′ and 3′ untranslated regions). A gene may be “isolated” by which is meant a nucleic acid that is substantially or essentially free from components normally found in association with the nucleic acid in its natural state. Such components include other cellular material, culture medium from recombinant production, and/or various chemicals used in chemically synthesizing the nucleic acid.

The term “genome” as used herein includes an organism's chromosomal/nuclear genome as well as any mitochondrial, and/or plasmid genome.

A “hairpin sequence” as used herein, is a nucleotide sequence comprising hairpins (e.g., that forms one or more hairpin structures). A hairpin (e.g., stem-loop, fold-back) refers to a nucleic acid molecule having a secondary structure that includes a region of complementary nucleotides that form a double strand that are further flanked on either side by single stranded-regions. Such structures are well known in the art. As known in the art, the double stranded region can comprise some mismatches in base pairing or can be perfectly complementary. In some embodiments of the present disclosure, a hairpin sequence of a nucleic acid construct can be located at the 3′end of a tracr nucleic acid.

A “heterologous” or a “recombinant” nucleotide sequence is a nucleotide sequence not naturally associated with a host cell into which it is introduced, including non-naturally occurring multiple copies of a naturally occurring nucleotide sequence.

Different nucleic acids or proteins having homology are referred to herein as “homologues.” The term homologue includes homologous sequences from the same and other species and orthologous sequences from the same and other species. “Homology” refers to the level of similarity between two or more nucleic acid and/or amino acid sequences in terms of percent of positional identity (i.e., sequence similarity or identity). Homology also refers to the concept of similar functional properties among different nucleic acids or proteins. Thus, the compositions and methods of the invention further comprise homologues to the nucleotide sequences and polypeptide sequences of this invention.

“Orthologous,” as used herein, refers to homologous nucleotide sequences and/or amino acid sequences in different species that arose from a common ancestral gene during speciation. A homologue of a nucleotide sequence of this invention has a substantial sequence identity (e.g., at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and/or 100%) to said nucleotide sequence of the invention. Thus, for example, a homologue of a Type I, Type II, Type III, Type IV, or Type V polynucleotide or polypeptide can be about 70% homologous or more to any one of any known or later identified Type I, Type II, Type III, Type IV, or Type V polynucleotide or polypeptide.

As used herein, hybridization, hybridize, hybridizing, and grammatical variations thereof, refer to the binding of two fully complementary nucleotide sequences or substantially complementary sequences in which some mismatched base pairs may be present. The conditions for hybridization are well known in the art and vary based on the length of the nucleotide sequences and the degree of complementarity between the nucleotide sequences. In some embodiments, the conditions of hybridization can be high stringency, or they can be medium stringency or low stringency depending on the amount of complementarity and the length of the sequences to be hybridized. The conditions that constitute low, medium and high stringency for purposes of hybridization between nucleotide sequences are well known in the art (See, e.g., Gasiunas et al. (2012) Proc. Natl. Acad. Sci. 109:E2579-E2586; M. R. Green and J. Sambrook (2012) Molecular Cloning: A Laboratory Manual. 4th Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.).

As used herein, the terms “increase,” “increasing,” “increased,” “enhance,” “enhanced,” “enhancing,” and “enhancement” (and grammatical variations thereof) describe an elevation of at least about 25%, 50%, 75%, 100%, 150%, 200%, 300%, 400%, 500% or more as compared to a control.

A “native” or “wild type” nucleic acid, nucleotide sequence, polypeptide or amino acid sequence refers to a naturally occurring or endogenous nucleic acid, nucleotide sequence, polypeptide or amino acid sequence. Thus, for example, a “wild type mRNA” is a mRNA that is naturally occurring in or endogenous to the organism. A “homologous” nucleic acid sequence is a nucleotide sequence naturally associated with a host cell into which it is introduced.

Also as used herein, the terms “nucleic acid,” “nucleic acid molecule,” “nucleic acid construct,” “nucleotide sequence” and “polynucleotide” refer to RNA or DNA that is linear or branched, single or double stranded, or a hybrid thereof. The term also encompasses RNA/DNA hybrids. When dsRNA is produced synthetically, less common bases, such as inosine, 5-methylcytosine, 6-methyladenine, hypoxanthine and others can also be used for antisense, dsRNA, and ribozyme pairing. For example, polynucleotides that contain C-5 propyne analogues of uridine and cytidine have been shown to bind RNA with high affinity and to be potent antisense inhibitors of gene expression. Other modifications, such as modification to the phosphodiester backbone, or the 2′-hydroxy in the ribose sugar group of the RNA can also be made. The nucleic acid constructs of the present disclosure can be DNA or RNA, but are preferably DNA. Thus, although the nucleic acid constructs of this invention may be described and used in the form of DNA, depending on the intended use, they may also be described and used in the form of RNA.

As used herein, the term “nucleotide sequence” refers to a heteropolymer of nucleotides or the sequence of these nucleotides from the 5′ to 3′ end of a nucleic acid molecule and includes DNA or RNA molecules, including cDNA, a DNA fragment or portion, genomic DNA, synthetic (e.g., chemically synthesized) DNA, plasmid DNA, mRNA, and anti-sense RNA, any of which can be single stranded or double stranded. The terms “nucleotide sequence” “nucleic acid,” “nucleic acid molecule,” “oligonucleotide” and “polynucleotide” are also used interchangeably herein to refer to a heteropolymer of nucleotides. Except as otherwise indicated, nucleic acid molecules and/or nucleotide sequences provided herein are presented herein in the 5′ to 3′ direction, from left to right and are represented using the standard code for representing the nucleotide characters as set forth in the U.S. sequence rules, 37 CFR §§ 1.821-1.825 and the World Intellectual Property Organization (WIPO) Standard ST.25.

As used herein, the term “percent sequence identity” or “percent identity” refers to the percentage of identical nucleotides in a linear polynucleotide sequence of a reference (“query”) polynucleotide molecule (or its complementary strand) as compared to a test (“subject”) polynucleotide molecule (or its complementary strand) when the two sequences are optimally aligned. In some embodiments, “percent identity” can refer to the percentage of identical amino acids in an amino acid sequence.

A “protospacer sequence” refers to the target double stranded DNA and specifically to the portion of the target DNA (e.g., or target region in the genome) that is fully or substantially complementary (and hybridizes) to the spacer sequence of the CRISPR repeat-spacer sequences, CRISPR repeat-spacer-repeat sequences, and/or CRISPR arrays.

As used herein, the terms “reduce,” “reduced,” “reducing,” “reduction,” “diminish,” “suppress,” and “decrease” (and grammatical variations thereof), describe, for example, a decrease of at least about 5%, 10%, 15%, 20%, 25%, 35%, 50%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% as compared to a control. In particular embodiments, the reduction can result in no or essentially no (i.e., an insignificant amount, e.g., less than about 10% or even 5%) detectable activity or amount of the component being measured (e.g., the population of cells or a genome size). Thus, for example, a reduced genome size can mean a reduction in the size of a genome of at least about 5%, 10%, 15%, 20%, 25%, 35%, 50%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% as compared to a control.

A control as used herein may be, for example, a population of bacterial, archaeal, algal or yeast cells that has not been transformed with a heterologous nucleic acid construct of this invention. In some embodiments, a control may be a wild-type population of bacterial, archaeal, algal or yeast cells, or it may be a population of bacterial, archaeal or yeast cells transformed with a heterologous construct comprising a CRISPR array comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer comprises a nucleotide sequence that is not complementary to a target region in the genome of the bacterial, archaeal or yeast cells of said population (i.e., non-self targeting/“scrambled spacer”). In additional aspects, a control may be, for example, a wild-type population of bacterial, archaeal, algal or yeast cells, or a population of bacterial, archaeal, algal or yeast cells transformed with a heterologous construct comprising a CRISPR array comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial, archaeal, algal or yeast cells of said population that is not located adjacent to a protospacer adjacent motif (PAM).

A “repeat sequence” as used herein refers, for example, to any repeat sequence of a wild-type CRISPR locus or a repeat sequence of a synthetic CRISPR array that are separated by “spacer sequences” (e.g., a repeat-spacer sequence or a repeat-spacer-repeat sequence of the invention). A repeat sequence useful with this invention can be any known or later identified repeat sequence of a CRISPR locus. Accordingly, in some embodiments, a repeat-spacer sequence or a repeat-spacer-repeat comprises a repeat that is substantially identical (e.g. at least about 70% identical (e.g., at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more)) to a repeat from a wild-type Type II CRISPR array. In some embodiments, a repeat sequence is 100% identical to a repeat from a wild type Type I CRISPR array, a wild type Type II CRISPR array, wild type Type III CRISPR array, wild type Type IV CRISPR array, or wild type Type V CRISPR array. In additional embodiments, a repeat sequence useful with this invention can comprise a nucleotide sequence comprising a partial repeat that is a fragment or portion of a consecutive nucleotides of a repeat sequence of a CRISPR locus or synthetic CRISPR array of any of a Type I crRNA, Type II crRNA, Type III crRNA, Type IV crRNA, or Type V crRNA.

As used herein, “CRISPR array” of a Type I, Type II, Type III, Type IV, or Type V CRISPR-Cas system refers to a nucleic acid construct that comprises from 5′ to 3′ a repeat-spacer-repeat sequence or comprises from 5′ to 3′ at least one repeat-spacer sequence (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 repeat-spacer sequences, and any range or value therein). When more than one repeat-spacer is comprised in a CRISPR array, the spacer of the prior (5′ to 3′) repeat-spacer sequence can be linked to the repeat of the following repeat-spacer (e.g., the spacer of a first repeat-spacer sequence is linked to the repeat of a second repeat-spacer sequence). In some embodiments, a CRISPR array can comprise two repeats (or two partial repeats) separated by a spacer (e.g., a repeat-spacer-repeat sequence).

As used herein “sequence identity” refers to the extent to which two optimally aligned polynucleotide or peptide sequences are invariant throughout a window of alignment of components, e.g., nucleotides or amino acids. “Identity” can be readily calculated by known methods including, but not limited to, those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, New York (1991).

A “spacer sequence” as used herein is a nucleotide sequence that is complementary to a target DNA (i.e., target region in the genome or the “protospacer sequence”, which is adjacent to a protospacer adjacent motif (PAM) sequence). The spacer sequence can be fully complementary or substantially complementary (e.g., at least about 70% complementary (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more)) to a target DNA. In representative embodiments, the spacer sequence has 100% complementarity to the target DNA. In additional embodiments, the complementarity of the 3′ region of the spacer sequence to the target DNA is 100% but is less than 100% in the 5′ region of the spacer and therefore the overall complementarity of the spacer sequence to the target DNA is less than 100%. Thus, for example, the first 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, and the like, nucleotides in the 3′ region of a 20 nucleotide spacer sequence (seed sequence) can be 100% complementary to the target DNA, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 70% complementary) to the target DNA. In some embodiments, the first 7 to 12 nucleotides of the spacer sequence can be 100% complementary to the target DNA, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 70% complementary) to the target DNA. In other embodiments, the first 7 to 10 nucleotides of the spacer sequence can be 100% complementary to the target DNA, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 70% complementary) to the target DNA. In representative embodiments, the first 7 nucleotides (within the seed) of the spacer sequence can be 100% complementary to the target DNA, while the remaining nucleotides in the 5′ region of the spacer sequence are substantially complementary (e.g., at least about 70% complementary) to the target DNA.

As used herein, a “target DNA,” “target region” or a “target region in the genome” refers to a region of an organism's genome that is fully complementary or substantially complementary (e.g., at least 70% complementary (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more)) to a spacer sequence in a repeat-spacer sequence or repeat-spacer-repeat sequence. In some embodiments, a target region may be about 10 to about 40 consecutive nucleotides in length located immediately adjacent to a PAM sequence (PAM sequence located immediately 3′ of the target region) in the genome of the organism (e.g., Type I CRISPR-Cas systems and Type II CRISPR-Cas systems). In the some embodiments, e.g., Type I systems, the PAM is on the alternate side of the protospacer (the 5′ end). There is no known PAM for Type III systems. Makarova et al. describes the nomenclature for all the classes, types and subtypes of CRISPR systems (Nature Reviews Microbiology 13:722-736 (2015)). Guide structures and PAMs are described in by R. Barrangou (Genome Biol. 16:247 (2015)).

In some embodiments, a target region useful with this invention is located within an essential gene or a non-essential gene.

In representative embodiments, a target region can be randomly selected or can be specifically selected. In some embodiments, a randomly selected target region may be selected from any at least 10 consecutive nucleotides (e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, and the like, and any range or value therein) located immediately adjacent to a PAM sequence in a bacterial, archaeal, algal or yeast genome. In some embodiments, the target region can be about 10 to about 20 consecutive nucleotides, about 10 to about 30 consecutive nucleotides, and/or about 10 to about 40 consecutive nucleotides and the like, or any range or value therein, located immediately adjacent to a protospacer adjacent motif (PAM) sequence in a bacterial, archaeal, algal or yeast genome. In some embodiments, specifically selecting a target region can comprise selecting two or more target regions that are located about every 100 nucleotides to about every 1000 nucleotides, about every 100 nucleotides to about every 2000, about every 100 nucleotides to about every 3000, about every 100 nucleotides to about every 4000, and/or about every 100 nucleotides to about every 5000 nucleotides, and the like, from one another in the genome of the one or more bacteria, archaea, algal or yeast cells. In particular embodiments, specifically selecting a target region comprises specifically selecting a target region from a gene, open reading frame, a putative open reading frame or an intergenic region comprising at least about 10 to about 40 consecutive nucleotides immediately adjacent to a PAM sequence in a bacterial, archaeal, algal or yeast genome.

A “trans-activating CRISPR (tracr) nucleic acid” or “tracr nucleic acid” as used herein refers to any tracr RNA (or its encoding DNA). A tracr nucleic acid comprises from 5′ to 3′ a lower stem, an upper stem, a bulge, a nexus hairpin and terminal hairpins (See, Briner et al. (2014) Molecular Cell. 56(2):333-339). A trans-activating CRISPR (tracr) nucleic acid functions in hybridizing to the repeat portion of mature or immature crRNAs, recruits Cas9 protein to the target site, and may facilitate the catalytic activity of Cas9 by inducting structural rearrangement. The functional composition of tracrRNA molecules is listed above. Sequences for tracrRNAs are specific to the CRISPR-Cas system and can be variable. Any tracr nucleic acid, known or later identified, can be used with this invention.

As used herein, the phrase “substantially identical,” or “substantial identity” in the context of two nucleic acid molecules, nucleotide sequences or protein sequences, refers to two or more sequences or subsequences that have at least about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and/or 100% nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection. In some embodiments of the invention, the substantial identity exists over a region of the sequences that is at least about 50 residues to about 150 residues in length. Thus, in some embodiments of the invention, the substantial identity exists over a region of the sequences that is at least about 3 to about 15 (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 residues in length and the like or any value or any range therein), at least about 5 to about 30, at least about 10 to about 30, at least about 16 to about 30, at least about 18 to at least about 25, at least about 18, at least about 22, at least about 25, at least about 30, at least about 40, at least about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120, about 130, about 140, about 150, or more residues in length, and any range therein. In representative embodiments, the sequences can be substantially identical over at least about 22 nucleotides. In some particular embodiments, the sequences are substantially identical over at least about 150 residues. In some embodiments, sequences of the invention can be about 70% to about 100% identical over at least about 16 nucleotides to about 25 nucleotides. In some embodiments, sequences of the invention can be about 75% to about 100% identical over at least about 16 nucleotides to about 25 nucleotides. In further embodiments, sequences of the invention can be about 80% to about 100% identical over at least about 16 nucleotides to about 25 nucleotides. In further embodiments, sequences of the invention can be about 80% to about 100% identical over at least about 7 nucleotides to about 25 nucleotides. In some embodiments, sequences of the invention can be about 70% identical over at least about 18 nucleotides. In other embodiments, the sequences can be about 85% identical over about 22 nucleotides. In still other embodiments, the sequences can be 100% identical over about 16 nucleotides. In a further embodiment, the sequences are substantially identical over the entire length of a coding region. Furthermore, in exemplary embodiments, substantially identical nucleotide or polypeptide sequences perform substantially the same function (e.g., the function or activity of a crRNA, tracr nucleic acid, repeat sequence, Cas9 nuclease (nickase, DNA, RNA and/or PAM recognition and binding), Cas3, Cas3′, Cas3″ or any other CRISPR-Cas polynucleotide or polypeptide).

For sequence comparison, typically one sequence acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.

Optimal alignment of sequences for aligning a comparison window are well known to those skilled in the art and may be conducted by tools such as the local homology algorithm of Smith and Waterman, the homology alignment algorithm of Needleman and Wunsch, the search for similarity method of Pearson and Lipman, and optionally by computerized implementations of these algorithms such as GAP, BESTFIT, FASTA, and TFASTA available as part of the GCG® Wisconsin Package® (Accelrys Inc., San Diego, Calif.). An “identity fraction” for aligned segments of a test sequence and a reference sequence is the number of identical components which are shared by the two aligned sequences divided by the total number of components in the reference sequence segment, i.e., the entire reference sequence or a smaller defined part of the reference sequence. Percent sequence identity is represented as the identity fraction multiplied by 100. The comparison of one or more polynucleotide sequences may be to a full-length polynucleotide sequence or a portion thereof, or to a longer polynucleotide sequence. For purposes of this invention “percent identity” may also be determined using BLASTX version 2.0 for translated nucleotide sequences and BLASTN version 2.0 for polynucleotide sequences.

Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., 1990). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when the cumulative alignment score falls off by the quantity X from its maximum achieved value, the cumulative score goes to zero or below due to the accumulation of one or more negative-scoring residue alignments, or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89: 10915 (1989)).

In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90: 5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a test nucleic acid sequence is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleotide sequence to the reference nucleotide sequence is less than about 0.1 to less than about 0.001. Thus, in some embodiments of the invention, the smallest sum probability in a comparison of the test nucleotide sequence to the reference nucleotide sequence is less than about 0.001.

Two nucleotide sequences can also be considered to be substantially complementary when the two sequences hybridize to each other under stringent conditions. In some representative embodiments, two nucleotide sequences considered to be substantially complementary hybridize to each other under highly stringent conditions.

“Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization experiments such as Southern and Northern hybridizations are sequence dependent, and are different under different environmental parameters. An extensive guide to the hybridization of nucleic acids is found in Tijssen Laboratory Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Acid Probes part I chapter 2 “Overview of principles of hybridization and the strategy of nucleic acid probe assays” Elsevier, New York (1993). Generally, highly stringent hybridization and wash conditions are selected to be about 5° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength and pH.

The T_(m) is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. Very stringent conditions are selected to be equal to the T_(m) for a particular probe. An example of stringent hybridization conditions for hybridization of complementary nucleotide sequences which have more than 100 complementary residues on a filter in a Southern or northern blot is 50% formamide with 1 mg of heparin at 42° C., with the hybridization being carried out overnight. An example of highly stringent wash conditions is 0.1 5M NaCl at 72° C. for about 15 minutes. An example of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15 minutes (see, Sambrook, infra, for a description of SSC buffer). Often, a high stringency wash is preceded by a low stringency wash to remove background probe signal. An example of a medium stringency wash for a duplex of, e.g., more than 100 nucleotides, is 1×SSC at 45° C. for 15 minutes. An example of a low stringency wash for a duplex of, e.g., more than 100 nucleotides, is 4-6×SSC at 40° C. for 15 minutes. For short probes (e.g., about 10 to 50 nucleotides), stringent conditions typically involve salt concentrations of less than about 1.0 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3, and the temperature is typically at least about 30° C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. In general, a signal to noise ratio of 2× (or higher) than that observed for an unrelated probe in the particular hybridization assay indicates detection of a specific hybridization. Nucleotide sequences that do not hybridize to each other under stringent conditions are still substantially identical if the proteins that they encode are substantially identical. This can occur, for example, when a copy of a nucleotide sequence is created using the maximum codon degeneracy permitted by the genetic code.

The following are examples of sets of hybridization/wash conditions that may be used to clone homologous nucleotide sequences that are substantially identical to reference nucleotide sequences of the invention. In one embodiment, a reference nucleotide sequence hybridizes to the “test” nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 2×SSC, 0.1% SDS at 50° C. In another embodiment, the reference nucleotide sequence hybridizes to the “test” nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 1×SSC, 0.1% SDS at 50° C. or in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.5×SSC, 0.1% SDS at 50° C. In still further embodiments, the reference nucleotide sequence hybridizes to the “test” nucleotide sequence in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 50° C., or in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO₄, 1 mM EDTA at 50° C. with washing in 0.1×SSC, 0.1% SDS at 65° C.

Any nucleotide sequence and/or heterologous nucleic acid construct of this invention can be codon optimized for expression in any species of interest. Codon optimization is well known in the art and involves modification of a nucleotide sequence for codon usage bias using species specific codon usage tables. The codon usage tables are generated based on a sequence analysis of the most highly expressed genes for the species of interest. When the nucleotide sequences are to be expressed in the nucleus, the codon usage tables are generated based on a sequence analysis of highly expressed nuclear genes for the species of interest. The modifications of the nucleotide sequences are determined by comparing the species specific codon usage table with the codons present in the native polynucleotide sequences. As is understood in the art, codon optimization of a nucleotide sequence results in a nucleotide sequence having less than 100% identity (e.g., 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to the native nucleotide sequence but which still encodes a polypeptide having the same function as that encoded by the original, native nucleotide sequence. Thus, in representative embodiments of the invention, the nucleotide sequence and/or heterologous nucleic acid construct of this invention can be codon optimized for expression in the particular species of interest.

In some embodiments, the heterologous or recombinant nucleic acids molecules, nucleotide sequences and/or polypeptides of the invention are “isolated.” An “isolated” nucleic acid molecule, an “isolated” nucleotide sequence or an “isolated” polypeptide is a nucleic acid molecule, nucleotide sequence or polypeptide that, by the hand of man, exists apart from its native environment and is therefore not a product of nature. An isolated nucleic acid molecule, nucleotide sequence or polypeptide may exist in a purified form that is at least partially separated from at least some of the other components of the naturally occurring organism or virus, for example, the cell or viral structural components or other polypeptides or nucleic acids commonly found associated with the polynucleotide. In representative embodiments, the isolated nucleic acid molecule, the isolated nucleotide sequence and/or the isolated polypeptide is at least about 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more pure.

In other embodiments, an isolated nucleic acid molecule, nucleotide sequence or polypeptide may exist in a non-native environment such as, for example, a recombinant host cell. Thus, for example, with respect to nucleotide sequences, the term “isolated” means that it is separated from the chromosome and/or cell in which it naturally occurs. A polynucleotide is also isolated if it is separated from the chromosome and/or cell in which it naturally occurs in and is then inserted into a genetic context, a chromosome and/or a cell in which it does not naturally occur (e.g., a different host cell, different regulatory sequences, and/or different position in the genome than as found in nature). Accordingly, the heterologous nucleic acid constructs, nucleotide sequences and their encoded polypeptides are “isolated” in that, by the hand of man, they exist apart from their native environment and therefore are not products of nature, however, in some embodiments, they can be introduced into and exist in a recombinant host cell.

In some embodiments, the heterologous or recombinant nucleic acid constructs of the invention are “synthetic.” A “synthetic” nucleic acid molecule, a “synthetic” nucleotide sequence or a “synthetic” polypeptide is a nucleic acid molecule, nucleotide sequence or polypeptide that is not found in nature but is created by the hand of man and is therefore not a product of nature.

In any of the embodiments described herein, the nucleotide sequences and/or heterologous nucleic acid constructs of the invention can be operatively associated with a variety of promoters and other regulatory elements for expression in various organisms cells. Thus, in representative embodiments, a nucleic acid construct of this invention can further comprise one or more promoters operably linked to one or more nucleotide sequences.

By “operably linked” or “operably associated” as used herein, it is meant that the indicated elements are functionally related to each other, and are also generally physically related. Thus, the term “operably linked” or “operably associated” as used herein, refers to nucleotide sequences on a single nucleic acid molecule that are functionally associated. Thus, a first nucleotide sequence that is operably linked to a second nucleotide sequence, means a situation when the first nucleotide sequence is placed in a functional relationship with the second nucleotide sequence. For instance, a promoter is operably associated with a nucleotide sequence if the promoter effects the transcription or expression of said nucleotide sequence. Those skilled in the art will appreciate that the control sequences (e.g., promoter) need not be contiguous with the nucleotide sequence to which it is operably associated, as long as the control sequences function to direct the expression thereof. Thus, for example, intervening untranslated, yet transcribed, sequences can be present between a promoter and a nucleotide sequence, and the promoter can still be considered “operably linked” to the nucleotide sequence.

A “promoter” is a nucleotide sequence that controls or regulates the transcription of a nucleotide sequence (i.e., a coding sequence) that is operably associated with the promoter. The coding sequence may encode a polypeptide and/or a functional RNA. Typically, a “promoter” refers to a nucleotide sequence that contains a binding site for RNA polymerase II and directs the initiation of transcription. In general, promoters are found 5′, or upstream, relative to the start of the coding region of the corresponding coding sequence. The promoter region may comprise other elements that act as regulators of gene expression. These include a TATA box consensus sequence, and often a CAAT box consensus sequence (Breathnach and Chambon, (1981) Annu. Rev. Biochem. 50:349). In plants, the CAAT box may be substituted by the AGGA box (Messing et al., (1983) in Genetic Engineering of Plants, T. Kosuge, C. Meredith and A. Hollaender (eds.), Plenum Press, pp. 211-227).

Promoters can include, for example, constitutive, inducible, temporally regulated, developmentally regulated, chemically regulated, tissue-preferred and/or tissue-specific promoters for use in the preparation of heterologous nucleic acid constructs, i.e., “chimeric genes” or “chimeric polynucleotides.” These various types of promoters are known in the art.

The choice of promoter will vary depending on the temporal and spatial requirements for expression, and also depending on the host cell to be transformed. Promoters for many different organisms are well known in the art. Based on the extensive knowledge present in the art, the appropriate promoter can be selected for the particular host organism of interest. Thus, for example, much is known about promoters upstream of highly constitutively expressed genes in model organisms and such knowledge can be readily accessed and implemented in other systems as appropriate.

In some embodiments, a nucleic acid construct of the invention can be an “expression cassette” or can be comprised within an expression cassette. As used herein, “expression cassette” means a heterologous nucleic acid construct comprising a nucleotide sequence of interest (e.g., the nucleic acid constructs of the invention (e.g., a synthetic tracr nucleic acid construct, a synthetic CRISPR nucleic acid construct, a synthetic CRISPR array, a chimeric nucleic acid construct; a nucleotide sequence encoding a polypeptide of interest, a Type I polypeptide, Type II polypeptide, Type III polypeptide, Type IV polypeptide, and/or Type V polypeptide)), wherein said nucleotide sequence is operably associated with at least a control sequence (e.g., a promoter). Thus, some aspects of the invention provide expression cassettes designed to express the nucleotides sequences of the invention.

An expression cassette comprising a nucleotide sequence of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. An expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression.

An expression cassette also can optionally include a transcriptional and/or translational termination region (i.e., termination region) that is functional in the selected host cell. A variety of transcriptional terminators are available for use in expression cassettes and are responsible for the termination of transcription beyond the heterologous nucleotide sequence of interest and correct mRNA polyadenylation. The termination region may be native to the transcriptional initiation region, may be native to the operably linked nucleotide sequence of interest, may be native to the host cell, or may be derived from another source (i.e., foreign or heterologous to the promoter, to the nucleotide sequence of interest, to the host, or any combination thereof).

An expression cassette also can include a nucleotide sequence for a selectable marker, which can be used to select a transformed host cell. As used herein, “selectable marker” means a nucleotide sequence that when expressed imparts a distinct phenotype to the host cell expressing the marker and thus allows such transformed cells to be distinguished from those that do not have the marker. Such a nucleotide sequence may encode either a selectable or screenable marker, depending on whether the marker confers a trait that can be selected for by chemical means, such as by using a selective agent (e.g., an antibiotic and the like), or on whether the marker is simply a trait that one can identify through observation or testing, such as by screening (e.g., fluorescence). Of course, many examples of suitable selectable markers are known in the art and can be used in the expression cassettes described herein.

In addition to expression cassettes, the nucleic acid molecules and nucleotide sequences described herein can be used in connection with vectors. The term “vector” refers to a composition for transferring, delivering or introducing a nucleic acid (or nucleic acids) into a cell. A vector comprises a nucleic acid molecule comprising the nucleotide sequence(s) to be transferred, delivered or introduced. Vectors for use in transformation of host organisms are well known in the art. Non-limiting examples of general classes of vectors include but are not limited to a viral vector, a plasmid vector, a phage vector, a phagemid vector, a cosmid vector, a fosmid vector, a bacteriophage, an artificial chromosome, or an Agrobacterium binary vector in double or single stranded linear or circular form which may or may not be self transmissible or mobilizable. A vector as defined herein can transform prokaryotic or eukaryotic host either by integration into the cellular genome or exist extrachromosomally (e.g. autonomous replicating plasmid with an origin of replication). Additionally included are shuttle vectors by which is meant a DNA vehicle capable, naturally or by design, of replication in two different host organisms, which may be selected from actinomycetes and related species, bacteria and eukaryotic (e.g. higher plant, mammalian, yeast or fungal cells). In some representative embodiments, the nucleic acid in the vector is under the control of, and operably linked to, an appropriate promoter or other regulatory elements for transcription in a host cell. The vector may be a bi-functional expression vector which functions in multiple hosts. In the case of genomic DNA, this may contain its own promoter or other regulatory elements and in the case of cDNA this may be under the control of an appropriate promoter or other regulatory elements for expression in the host cell. Accordingly, the nucleic acid molecules of this invention and/or expression cassettes can be comprised in vectors as described herein and as known in the art.

“Introducing,” “introduce,” “introduced” (and grammatical variations thereof) in the context of a polynucleotide of interest means presenting the polynucleotide of interest to the host organism or cell of said organism (e.g., host cell) in such a manner that the polynucleotide gains access to the interior of a cell. Where more than one polynucleotide is to be introduced these polynucleotides can be assembled as part of a single polynucleotide or nucleic acid construct, or as separate polynucleotide or nucleic acid constructs, and can be located on the same or different expression constructs or transformation vectors. Accordingly, these polynucleotides can be introduced into cells in a single transformation event, in separate transformation/transfection events, or, for example, they can be incorporated into an organism by conventional breeding protocols. Thus, in some aspects, one or more nucleic acid constructs of this invention can be introduced singly or in combination into a host organism or a cell of said host organism. In the context of a population of cells, “introducing” means contacting the population with the heterologous nucleic acid constructs of the invention under conditions where the heterologous nucleic acid constructs of the invention gain access to the interior of one or more cells of the population, thereby transforming the one or more cells of the population.

The term “transformation” or “transfection” as used herein refers to the introduction of a heterologous nucleic acid into a cell. Transformation of a cell may be stable or transient. Thus, in some embodiments, a host cell or host organism is stably transformed with a nucleic acid construct of the invention. In other embodiments, a host cell or host organism is transiently transformed with a nucleic acid construct of the invention. Thus, in representative embodiments, a heterologous nucleic acid construct of the invention can be stably and/or transiently introduced into a cell.

“Transient transformation” in the context of a polynucleotide means that a polynucleotide is introduced into the cell and does not integrate into the genome of the cell.

By “stably introducing” or “stably introduced,” in the context of a polynucleotide, means that the introduced polynucleotide is stably incorporated into the genome of the cell, and thus the cell is stably transformed with the polynucleotide.

“Stable transformation” or “stably transformed” as used herein means that a nucleic acid construct is introduced into a cell and integrates into the genome of the cell. As such, the integrated nucleic acid construct is capable of being inherited by the progeny thereof, more particularly, by the progeny of multiple successive generations. “Genome” as used herein includes the nuclear, mitochondrial and plasmid genome, and therefore may include integration of a nucleic acid construct into, for example, the plasmid or mitochondrial genome. Stable transformation as used herein may also refer to a transgene that is maintained extrachromasomally, for example, as a minichromosome or a plasmid.

Transient transformation may be detected by, for example, an enzyme-linked immunosorbent assay (ELISA) or Western blot, which can detect the presence of a peptide or polypeptide encoded by one or more transgene introduced into an organism. Stable transformation of a cell can be detected by, for example, a Southern blot hybridization assay of genomic DNA of the cell with nucleic acid sequences which specifically hybridize with a nucleotide sequence of a transgene introduced into an organism (e.g., a bacterium, an archaea, a yeast, an algae, and the like). Stable transformation of a cell can be detected by, for example, a Northern blot hybridization assay of RNA of the cell with nucleic acid sequences which specifically hybridize with a nucleotide sequence of a transgene introduced into a plant or other organism. Stable transformation of a cell can also be detected by, e.g., a polymerase chain reaction (PCR) or other amplification reactions as are well known in the art, employing specific primer sequences that hybridize with target sequence(s) of a transgene, resulting in amplification of the transgene sequence, which can be detected according to standard methods. Transformation can also be detected by direct sequencing and/or hybridization protocols well known in the art.

Accordingly, in some embodiments, the nucleotide sequences, constructs, expression cassettes can be expressed transiently and/or they can be stably incorporated into the genome of the host organism.

A heterologous nucleic acid construct of the invention can be introduced into a cell by any method known to those of skill in the art. In some embodiments of the invention, transformation of a cell comprises nuclear transformation. In still further embodiments, the heterologous nucleic acid construct (s) of the invention can be introduced into a cell via conventional breeding techniques.

Procedures for transforming both eukaryotic and prokaryotic organisms are well known and routine in the art and are described throughout the literature (See, for example, Jiang et al. 2013. Nat. Biotechnol. 31:233-239; Ran et al. Nature Protocols 8:2281-2308 (2013))

A nucleotide sequence therefore can be introduced into a host organism or its cell in any number of ways that are well known in the art. The methods of the invention do not depend on a particular method for introducing one or more nucleotide sequences into the organism, only that they gain access to the interior of at least one cell of the organism. Where more than one nucleotide sequence is to be introduced, they can be assembled as part of a single nucleic acid construct, or as separate nucleic acid constructs, and can be located on the same or different nucleic acid constructs. Accordingly, the nucleotide sequences can be introduced into the cell of interest in a single transformation event, or in separate transformation events, or, alternatively, where relevant, a nucleotide sequence can be incorporated into an organism as part of a breeding protocol.

Mobile genetic elements (MGEs) present bacteria with continuous challenges to genomic stability, promoting evolution through horizontal gene transfer. The term MGE encompasses plasmids, bacteriophages, transposable elements, genomic islands, and many other specialized genetic elements (1). MGEs encompass genes conferring high rates of dissemination, adaptive advantages to the host, and genomic stability, leading to their near universal presence in bacterial genomes. To cope with the permanent threat of predatory bacteriophages and selfish genetic elements, bacteria have evolved both innate and adaptive immune systems targeting exogenous genetic elements. Innate immunity includes cell-wall modification, restriction/modification systems, and abortive phage infection (2). Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas) are an adaptive immune system targeted against invasive genetic elements in bacteria (3). CRISPR-Cas mediated immunity relies on distinct molecular processes, categorized as acquisition, expression, and interference (3). Acquisition occurs via molecular ‘sampling’ of foreign genetic elements, from which short sequences, termed spacers, are integrated in a polarized fashion into the CRISPR array (4). Expression of CRISPR arrays is constitutive and inducible by promoter elements within the preceding leader sequence (5-6). Interference results from a corresponding transcript that is processed selectively at each repeat sequence, forming CRISPR RNAs (crRNAs) that guide Cas proteins for sequence-specific recognition and cleavage of target DNA complementary to the spacer (7). CRISPR-Cas technology has applications in strain typing and detection (8-10), exploitation of natural/engineered immunity against mobile genetic elements (11), programmable genome editing in diverse backgrounds (12), transcriptional control (13-14), and manipulation of microbial populations in defined consortia (15).

The various CRISPR systems are known in the art. For example, see Makarova et al., which describes the nomenclature for all the classes, types and subtypes of CRISPR systems (Nature Reviews Microbiology 13:722-736 (2015)); see also, R. Barrangou (Genome Biol. 16:247 (2015)).

Although sequence features corresponding to CRISPR arrays were described previously in multiple organisms (16-17), Streptococcus thermophilus was the first microbe where the roles of specific cas genes and CRISPR-array components were elucidated (4). S. thermophilus is a non-pathogenic thermophilic Gram-positive bacterium used as a starter culture that catabolizes lactose to lactic acid in the syntrophic production of yogurt and various cheeses (18). S. thermophilus encodes up to four CRISPR-Cas systems, two of them (SthCRISPR1 and SthCRISPR3) are classified as Type II-A systems that are innately active in both acquisition and interference (4, 19). Accordingly, genomic analysis of S. thermophilus and its bacteriophages established a likely mechanism of CRISPR-Cas systems for phage/DNA protection. Investigation of CRISPR-Cas systems in S. thermophilus led to bioinformatic analysis of spacer origin (4, 20), discovery of the proto-spacer adjacent motif (PAM) sequences (19; 21), understanding of phage-host dynamics (22-23), demonstration of Cas9 endonuclease activity (7, 24-25), and recently, determination of the tracrRNA structural motifs governing function and orthogonality of Type II systems (26). Genomic analysis of S. thermophilus revealed evolutionary adaptation to milk through loss of carbohydrate catabolism and virulence genes found in pathogenic streptococci (18). S. thermophilus also underwent significant acquisition of niche-related genes, such as those encoding including cold-shock proteins, copper resistance proteins, proteinases, bacteriocins, and lactose catabolism proteins (18). Insertion sequences (ISs) are highly prevalent in S. thermophilus genomes and contribute to genetic heterogeneity between strains by facilitating dissemination of islands associated with dairy adaptation genes (18). The concomitant presence of MGEs and functional CRISPR-Cas systems in S. thermophilus suggests that genome homeostasis is governed at least in part by the interplay of these dynamic forces. Thus, S. thermophilus constitutes an ideal host for investigating the genetic outcomes of CRISPR-Cas targeting of genomic islands.

CRISPR-Cas systems have recently been the subject of intense research in genome editing applications (12), but the evolutionary roles of most endogenous microbial systems remain unknown (27). Even less is known concerning evolutionary outcomes of housing active CRISPR-Cas systems beyond the prevention of foreign DNA uptake (7), spacer acquisition events (4), and mutation caused by chromosomal self-targeting (28-32). Thus, the present inventors sought to determine the outcomes of targeting integrated MGEs with endogenous Type II CRISPR-Cas systems. Four islands were identified in S. thermophilus LMD-9, with lengths ranging from 8 to 102 kbp and totaling approximately 132 kbp, or 7% of the genome. In order to target genomic islands, plasmid-based expression of engineered CRISPR arrays with self-targeting spacers were transformed into S. thermophilus LMD-9. Collectively, our results elucidate fundamental genetic outcomes of self-targeting events and show that CRISPR-Cas systems can direct genome evolution at the bacterial population level.

Utilizing these discoveries, the present inventors have developed novel methods for screening populations of bacterial, archaeal, algal or yeast cells for essential genes, non-essential genes, and/or expendible genomic islands; for killing one or more cells within a population of bacterial, archaeal, algal or yeast cells; for identifying a phenotype of a bacterial, archaeal, algal or yeast gene; for selecting one or more bacterial, archaeal, algal or yeast cells having a reducing the genome size from a population of bacterial, archaeal or yeast cells; and/or for identifying in a population of bacterial, archaeal, algal or yeast cells at least one isolate having a mutation (e.g., deletion) in its genome.

Thus in one aspect, the present inventors, have developed methods for identifying genetic variants in a population that have altered genetic content that provides them the ability to escape targeting. Here, the target sequence has been modified, and one looks for survivors that have that modification. In some aspects, the modification (i.e., mutation) is a deletion. Further, if the target sequence has been modified, then the wild type genotype is not essential.

Accordingly, in one aspect of the invention a method of screening a population of bacterial cells for essential genes, non-essential genes, and/or expendable genomic islands is provided, comprising: introducing into said population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial cells of said population, thereby producing a population of transformed bacterial cells; and determining the presence or absence of a deletion in the population of transformed bacterial cells, wherein the presence of a deletion in the population of transformed bacterial cells indicates that the target region is comprised within a non-essential gene and/or an expendable genomic island, and the absence of a deletion in the population means that the target region is comprised within an essential gene. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

In additional aspects, the invention provides a method of screening a population of bacterial, archaeal, algal or yeast cells for essential genes, non-essential genes, and/or expendable genomic islands, comprising: introducing into the population of bacterial, archaeal, algal or yeast cells: (a) a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, thereby producing a population of transformed bacterial, archaeal, algal or yeast cells; and determining the presence or absence of a deletion in the population of transformed bacterial, archaeal, algal or yeast cells, wherein the presence of a deletion in the population of transformed bacterial, archaeal or yeast cells means that the target region is comprised within a non-essential gene and/or an expendable genomic island, and the absence of a deletion in the population of transformed bacterial, archaeal, algal or yeast cells means that the target region is comprised within an essential gene.

In other aspects, a method of killing one or more bacterial cells within a population of bacterial cells is provided, comprising: introducing into the population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial cells of said population, thereby killing one or more bacterial cells that comprise the target region within the population. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

In an additional aspect, a method of killing one or more cells within a population of bacterial, archaeal, algal or yeast cells is provided, the method comprising: introducing into the population of bacterial, archaeal or yeast cells (a) a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of the at least one repeat-spacer sequence and repeat-spacer-repeat sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, thereby killing one or more cells that comprise the target region in their genome within the population of bacterial, archaeal, algal or yeast cells.

Transformation of bacterial genome-targeting CRISPR RNAs can be used to selectively kill bacterial cells on a sequence-specific basis to subtract genetically distinct subpopulations, thereby enriching bacterial populations lacking the target sequence. This distinction can occur on the basis of the heterogeneous distribution of orthogonal CRISPR-Cas systems within genetically similar populations. Thus, in some embodiments, an CRISPR array that is introduced into a population of cells can be compatible (i.e., functional) with a CRISPR-Cas system in the one or more bacterial cells to be killed but is not compatible (i.e., not functional) with the CRISPR Cas system of at least one or more bacterial cells in the population. For instance, Escherichia coli and Klebsiella pneumoniae can exhibit either Type I-E or Type I-F CRISPR-Cas systems; Clostridium difficile encodes Type I-B systems, and different strains of S. thermophilus exhibit both Type II-A and Type I-E systems or just Type II-A systems. Depending on the specific CRISPR RNA transformed into a mixture of bacteria, it can specifically target that subset of the population based on its functional compatibility with its cognate system. This can be applied to diverse species containing endogenous CRISPR-Cas systems such as, but not limited to: Pseudomonas spp. (such as: P. aeruginosa), Escherichia spp. (such as: E. coli), Enterobacter spp. (such as: E. cloacae), Staphylococcus spp. (such as: S. aureus), Enterococcus spp. (such as: E. faecalis, E. faecium), Streptomyces spp. (such as: S. somaliensis), Streptococcus spp. (such as: S. pyogenes), Vibrio spp. (such as: V. cholerae), Yersinia spp. (such as: Y. pestis), Francisella spp. (such as: F. tularensis, F. novicida), Bacillus spp. (such as: B. anthracis, B. cereus), Lactobacillus spp. (such as: L. casei, L. reuteri, L. acidophilus, L. rhamnosis), Burkholderia spp. (such as: B. mallei, B. pseudomallei), Klebsiella spp. (such as: K. pneumoniae), Shigella spp. (such as: S. dysenteriae, S. sonnei), Salmonella spp. (such as: S. enterica), Borrelia spp. (such as: B. burgdorfieri), Neisseria spp. (such as: N. meningitidis), Fusobacterium spp. (such as: F. nucleatum), Helicobacter spp. (such as: H. pylori), Chlamydia spp. (such as: C. trachomatis), Bacteroides spp. (such as: B. fragilis), Bartonella spp. (such as: B. quintana), Bordetella spp. (such as: B. pertussis), Brucella spp. (such as: B. abortus), Campylobacter spp. (such as: C. jejuni), Clostridium spp. (such as: C. difficile), Bifidobacterium spp. (such as: B. infantis), Haemophilus spp. (such as: H. influenzae), Listeria spp. (such as: L. monocytogenes), Legionella spp. (such as: L. pneumophila), Mycobacterium spp. (such as: M. tuberculosis), Mycoplasma spp. (such as: M. pneumoniae), Rickettsia spp. (such as: R. rickettsia), Acinetobacter spp. (such as: A. calcoaceticus, A. baumanii), Rumincoccus spp. (such as: R. albus), Propionibacterium spp. (such as: P. freudenreichii), Corynebacterium spp. (such as: C. diphtheriae), Propionibacterium spp. (such as: P. acnes), Brevibacterium spp. (such as: B. iodinum), Micrococcus spp. (such as: M. luteus), and/or Prevotella spp. (such as: P. histicola).

CRISPR targeting can remove specific bacterial subsets on the basis of the distinct genetic content in mixed populations. Support for this claim is presented in examples 4, 5 where Lac⁻ bacteria are selected for while Lac⁺ are removed from the population. The genetic distinction between the Lac⁺ and Lac⁻ strains is presented in examples 8 and 10, where sequencing of the surviving clones revealed up to 5.5% difference in genetic content compared to the reference wild-type S. thermophilus strain. CRISPR-targeting spacers can thus be tuned to various levels of bacterial relatedness by targeting conserved or divergent genetic sequences. Thus, in some embodiments, the bacterial cells in the population can comprise the same CRISPR Cas system and the introduced CRISPR array thus may be functional in the bacterial population as a whole but the genetic content of the different strains or species that make up the bacterial population is sufficiently distinct such that the target region for the introduced CRISPR array is found only in the one or more bacterial species of the population that is to be killed. This can be applied to diverse species containing endogenous CRISPR-Cas systems such as, but not limited to: Pseudomonas spp. (such as: P. aeruginosa), Escherichia spp. (such as: E. coli), Enterobacter spp. (such as: E. cloacae), Staphylococcus spp. (such as: S. aureus), Enterococcus spp. (such as: E. faecalis, E. faecium), Streptomyces spp. (such as: S. somaliensis), Streptococcus spp. (such as: S. pyogenes), Vibrio spp. (such as: V. cholerae), Yersinia spp. (such as: Y. pestis), Francisella spp. (such as: F. tularensis, F. novicida), Bacillus spp. (such as: B. anthracis, B. cereus), Lactobacillus spp. (such as: L. casei, L. reuteri, L. acidophilus, L. rhamnosis), Burkholderia spp. (such as: B. mallei, B. pseudomallei), Klebsiella spp. (such as: K. pneumoniae), Shigella spp. (such as: S. dysenteriae, S. sonnei), Salmonella spp. (such as: S. enterica), Borrelia spp. (such as: B. burgdorfieri), Neisseria spp. (such as: N. meningitidis), Fusobacterium spp. (such as: F. nucleatum), Helicobacter spp. (such as: H. pylori), Chlamydia spp. (such as: C. trachomatis), Bacteroides spp. (such as: B. fragilis), Bartonella spp. (such as: B. quintana), Bordetella spp. (such as: B. pertussis), Brucella spp. (such as: B. abortus), Campylobacter spp. (such as: C. jejuni), Clostridium spp. (such as: C. difficile), Bifidobacterium spp. (such as: B. infantis), Haemophilus spp. (such as: H. influenzae), Listeria spp. (such as: L. monocytogenes), Legionella spp. (such as: L. pneumophila), Mycobacterium spp. (such as: M. tuberculosis), Mycoplasma spp. (such as: M. pneumoniae), Rickettsia spp. (such as: R. rickettsia), Acinetobacter spp. (such as: A. calcoaceticus, A. baumanii), Rumincoccus spp. (such as: R. albus), Propionibacterium spp. (such as: P. freudenreichii), Corynebacterium spp. (such as: C. diphtheriae), Propionibacterium spp. (such as: P. acnes), Brevibacterium spp. (such as: B. iodinum), Micrococcus spp. (such as: M. luteus), and/or Prevotella spp. (such as: P. histicola).

The extent of killing within a population using the methods of this invention may be affected by the amenability of the particular population to transformation in addition to whether the target region is comprised in a non-essential gene, an essential gene or an expendable island. The extent of killing in a population of bacterial, archaeal or yeast cells can vary, for example, by organism, by genus and species. Accordingly, as used herein “killing” means eliminating 2 logs or more of the cells in a population (1% survival or less). Less than 1 log of killing would be a small reduction in the population; whereas 2-3 logs of killing results in a significant reduction of the population; and more than 3 logs of killing indicates that the population has been substantially eradicated.

In another aspect, a method of identifying a phenotype associated with a bacterial gene is provided, comprising: introducing into a population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of the at least one repeat-spacer sequence and repeat-spacer-repeat sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial cells of said population, wherein the target region comprises at least a portion of an open reading frame encoding a polypeptide or functional nucleic acid, thereby killing the cells comprising the target region and producing a population of transformed bacterial cells without the target region (i.e., surviving cells do not comprise the target region); and (i) analyzing the phenotype of the population of cells, or (ii) growing individual bacterial colonies from the population of transformed bacterial cells and analyzing the phenotype of the individual colonies. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

In another aspect, a method of identifying the phenotype of a bacterial, archaeal, algal, or yeast gene is provided, comprising: introducing into a population of bacterial, archaeal, algal or yeast cells (a) a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, thereby killing the bacterial, archaeal, algal or yeast cells comprising the target region and producing a population of transformed bacterial, archaeal, algal or yeast cells without the target region; and (i) analyzing the phenotype of the population of cells, and/or (ii) growing individual bacterial, archaeal, or yeast colonies from the population of transformed bacterial, archaeal, algal or yeast cells; and analyzing the phenotype of the individual colonies.

In some embodiments, the analysis comprises PCR, optical genome mapping, genome sequencing, restriction mapping and/or restriction analysis to identify and characterize the mutation, and complementation analysis and/or phenotypic assays to analyze the phenotype.

In some embodiments of the invention determining the extent of killing or a reduction in a population can comprise any method for determining population number, including, but not limited to, (1) plating the cells and counting the colonies, (2) optical density, (3) microscope counting, (4) most probable number, and/or (5) methylene blue reduction. In some embodiments, 16S rDNA sequencing can be used to profile a composition of mixed populations. This can be done, for example, by purifying DNA from the sample as a whole, and performing either whole-genome shotgun sequencing using high-throughput technologies or, for example, by PCR amplifying the 16S gene and sequencing the products in the same manner. The sequences can then be computationally assigned to certain bacterial taxa. In other embodiments, quantitative PCR methods may also be used to quantify bacterial levels. Such techniques are well known in the art. For example, primers for qPCR can be designed to amplify specifically from a strain species, genus, or group of organisms that share the sequence. Thus, a threshold number (ct) may be used to quantify said organism or group of organisms. In additional embodiments, any bacterial activity (phenotype) specific to the target population may also be used as a metric to determine depletion of a population.

In further embodiments, a method of selecting one or more bacterial cells having a reduced genome size from a population of bacterial cells is provided, comprising: introducing into a population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population, wherein the cells comprising the target region are killed, thereby selecting one or more bacterial cells without the target region and having a reduced genome size from the population of bacterial cells. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

In some embodiments, a method of selecting one or more bacterial cells having a reduced genome size from a population of bacterial cells, comprising: introducing into a population of bacterial cells: (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial cells, or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and (b) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population, the target region is located between the one or more heterologous nucleic acid constructs introduced into the genome, and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, wherein cells comprising the target region are killed and cells not comprising the target region survive, thereby selecting one or more bacterial cells without the target region and having a reduced genome size from the population of transgenic bacterial cells. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

As is well known in the art, transposons can be created via, for example, PCR amplification or through designed DNA synthesis, and may be introduced via any method of transformation.

In some embodiments, the invention provides a method of selecting one or more bacterial, archaeal, algal or yeast cells having a reduced genome size from a population of bacterial, archaeal, algal or yeast cells, comprising: introducing into a population of bacterial, archaeal or yeast cells (a) a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid, (b) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of the at least one repeat-spacer sequence and the at least one repeat-spacer-repeat sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial, archaeal, algal or yeast cells of said population, and (c) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein cells comprising the target region are killed, thereby selecting one or more bacterial, archaeal, algal or yeast cells without the target region and having a reduced genome size from the population of bacterial, archaeal, algal or yeast cells.

In other embodiments, a method of selecting one or more bacterial, archaeal, algal or yeast cells having a reduced genome size from a population of bacterial, archaeal, algal or yeast cells is provided, comprising: introducing into a population of bacterial, archaeal, algal or yeast cells: (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial, archaeal, algal or yeast cells, or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial, archaeal, algal or yeast cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and (b)(i) a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid, (ii) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of the at least one repeat-spacer sequence or the at least one repeat-spacer-repeat sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial, archaeal, algal or yeast cells of said population, and (iii) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein the target region is located between the one or more heterologous nucleic acid constructs incorporated into the genome, and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, wherein cells comprising the target region are killed and cells not comprising the target region survive, thereby selecting one or more bacterial, archaeal, algal or yeast cells without the target region and having a reduced genome size from the population of transgenic bacterial, archaeal, algal or yeast cells.

In some aspects, the reduced genome size may be reduced as compared to a control. In some aspects, a control may be a wild-type population of bacterial, archaeal, algal or yeast cells, or a population of bacterial, archaeal, algal or yeast cells transformed with a heterologous construct comprising a CRISPR array (e.g., a Type I, Type II, Type III, Type IV or Type V CRISPR array) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is not complementary to a target region in the genome of the bacterial, archaeal, algal or yeast cells of said population (i.e., non-self targeting/“scrambled spacer”). In additional aspects, a control may be a population of bacterial, archaeal, algal or yeast cells transformed with a heterologous construct comprising a CRISPR array comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of the bacterial, archaeal, algal or yeast cells of said population but lacks a protospacer adjacent motif (PAM).

In some embodiments, a method of identifying in a population of bacteria at least one isolate having a deletion in its genome (e.g., a chromosomal and/or plasmid deletion) is provided, comprising: introducing into a population of bacterial cells a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or said at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population and cells comprising the target region are killed, thereby producing a population of transformed bacterial cells without the target region; and growing individual bacterial colonies from the population of transformed bacterial cells, thereby identifying at least one isolate from the population of transformed bacteria having a deletion in its genome. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

In additional embodiments, the invention provides a method of identifying in a population of bacteria at least one isolate having a deletion in its genome, comprising: introducing into the population of bacterial cells: (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial cells, or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and b) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial cells of said population, wherein the target region is located between the one or more heterologous nucleic acid constructs introduced into the genome and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, and cells comprising the target region are killed [and cells not comprising the target region survive], thereby producing a population of transformed bacterial cells without the target region; and growing individual bacterial colonies from the population of transformed bacterial cells, thereby identifying at least one isolate from the population of bacteria having a deletion in its genome. A CRISPR array useful with this invention may be Type I, Type II, Type III, Type IV or Type V CRISPR array.

In further embodiments, a method of identifying in a population of bacterial, archaeal, algal or yeast cells at least one isolate having a deletion in its genome is provided, comprising: introducing into a population of bacterial, archaeal, algal or yeast cells: (a) a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid; (b) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer of said repeat-spacer-repeat sequence or at least one repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in the genome (e.g., chromosomal, mitochondrial and/or plasmid genome) of the bacterial, archaeal, algal or yeast cells of said population; and (c) a Cas9 polypeptide or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein cells comprising the target region are killed, thereby producing a population of transformed bacterial, archaeal, algal or yeast cells without the target region; and growing individual bacterial, archaeal or yeast colonies from the population of transformed bacterial, archaeal, algal or yeast cells, thereby identifying at least one isolate from the population of transformed bacterial, archaeal, algal or yeast cells having a deletion in its genome.

In still further embodiments, the invention provides a method of identifying in a population of bacterial, archaeal, algal or yeast cells at least one isolate having a deletion in its genome, comprising: introducing into the population of bacterial, archaeal, algal or yeast cells: (a)(i) one or more heterologous nucleic acid constructs comprising a nucleotide sequence having at least 80 percent identity to at least 300 consecutive nucleotides present in the genome of said bacterial, archaeal, algal or yeast cells, or (ii) two or more heterologous nucleic acid constructs comprising at least one transposon, thereby producing a population of transgenic bacterial, archaeal, algal or yeast cells comprising a non-natural site for homologous recombination between the one or more heterologous nucleic acid constructs integrated into the genome and the at least 300 consecutive nucleotides present in the genome, or between a first and a second transposon integrated into the genome; and (b)(i) a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid, (ii) a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) comprising a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, wherein the spacer comprises a nucleotide sequence that is substantially complementary to a target region in the genome of one or more bacterial, archaeal, algal or yeast cells of said population; and (iii) a Cas9 polypeptide and/or a heterologous nucleic acid construct comprising a polynucleotide encoding a Cas9 polypeptide, wherein the target region is located between the one or more heterologous nucleic acid constructs incorporated into the genome and the at least 300 consecutive nucleotides present in the genome and/or between the first transposon and second transposon, and cells comprising the target region are killed and cells not comprising the target region survive, thereby producing a population of transformed bacterial, archaeal, algal or yeast cells without the target region; and growing individual bacterial, archaeal or yeast colonies from the population of transformed bacterial, archaeal, algal or yeast cells, thereby identifying at least one isolate from the population having a deletion in its genome.

In some embodiments, fitness/growth rate can be increased by reducing genome size or by deleting select genes (encoding polypeptides or functional nucleic acids (e.g., transcriptional regulators)) that require high energy input for transcription and translation. Thus, in some embodiments, a method of increasing the fitness or growth rate of a population of bacterial, archaeal, algal or yeast cells is provided, comprising: selecting for a reduced genome size (e.g., selecting for the absence of a portion of the genome) and/or deletion in the genomes of the bacterial, archaeal, algal or yeast cells of the populations as described herein. In some embodiments, the deletion may comprise one gene or more than one gene. Therefore, through reducing the genome size or deleting a particular gene or genes, the cells of the population no longer expend energy on the transcription/translation of the portion of the genome that is absent or the deleted gene or genes, thereby having reduced energy needs and increased fitness as compared to a control population still comprising said portion of the genome and/or said gene or genes.

In other embodiments, a method of increasing the amount of a product produced from a population of bacterial, archaeal, algal or yeast cells is provided, comprising increasing the fitness or growth rate of the cell by selecting for a deletion in the genomes of the bacterial, archaeal, algal or yeast cells as described herein. In some embodiments, the products can include, but are not limited to, antibiotics, secondary metabolites, vitamins, proteins, enzymes, acids, and pharmaceuticals.

In some embodiments, a CRISPR array (crRNA, crDNA) useful with this invention may be an array from any Type I CRISPR-Cas system, Type II CRISPR-Cas system, Type III CRISPR-Cas system, Type IV CRISPR-Cas system, or a Type V CRISPR-Cas system.

With regard to the preceding embodiments, a heterologous nucleic acid construct comprising a tracr nucleic acid and a heterologous nucleic acid construct comprising a CRISPR array may be comprised in and introduced in the same construct (e.g., expression cassette or vector) or in different constructs. In particular embodiments, a heterologous nucleic acid construct comprising a tracr nucleic acid and a heterologous nucleic acid construct comprising a CRISPR array may be comprised in single construct (e.g., expression cassette and/or vector) that may optionally further comprise a polynucleotide encoding Cas9 polypeptide. In some embodiments, the heterologous nucleic acid construct comprising a tracr nucleic acid and the heterologous nucleic acid construct comprising a CRISPR array may be operably linked to a single promoter and/or to separate promoters.

In some embodiments, a heterologous nucleic acid construct comprising a trans-activating CRISPR (tracr) nucleic acid and a heterologous nucleic acid construct comprising a CRISPR array (crRNA, crDNA) may be comprised in a CRISPR guide (gRNA, gDNA). In some embodiments, a CRISPR guide may be operably linked to a promoter.

In some embodiments, a Cas9 polypeptide useful with this invention comprises at least 70% identity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to an amino acid sequence of a Cas9 nuclease. Exemplary Cas9 nucleases useful with this invention can be any Cas9 nuclease known to catalyze DNA cleavage in a CRISPR-Cas system. As known in the art, such Cas9 nucleases comprise a HNH motif and a RuvC motif (See, e.g., WO2013/176772; WO/2013/188638). In some embodiments, a functional fragment of a Cas9 nuclease can be used with this invention.

CRISPR-Cas systems and groupings of Cas9 nucleases are well known in the art and include, for example, a Streptococcus thermophilus CRISPR 1 (Sth CR1) group of Cas9 nucleases, a Streptococcus thermophilus CRISPR 3 (Sth CR3) group of Cas9 nucleases, a Lactobacillus buchneri CD034 (Lb) group of Cas9 nucleases, and a Lactobacillus rhamnosus GG (Lrh) group of Cas9 nucleases. Additional Cas9 nucleases include, but are not limited to, those of Lactobacillus curvatus CRL 705. Still further Cas9 nucleases useful with this invention include, but are not limited to, a Cas9 from Lactobacillus animalis KCTC 3501, and Lactobacillus farciminis WP 010018949.1.

Furthermore, in particular embodiments, the Cas9 nuclease can be encoded by a nucleotide sequence that is codon optimized for the organism comprising the target DNA. In still other embodiments, the Cas9 nuclease can comprise at least one nuclear localization sequence.

In some embodiments, a Type I polypeptide useful with this invention comprises at least 70% identity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to an amino acid sequence of a Cas3, Cas3′ nuclease, a Cas3″ nuclease, fusion variants thereof. In some embodiments, a Type I Cascade polypeptide useful with this invention comprises at least 70% identity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to an amino acid sequence of a Cas7 (Csa2), Cas8a1 (Csx13), Cas8a2 (Csx9), Cas5, Csa5, Cas6a, Cas6b, Cas8b (Csh1), Cas7 (Csh2), Cas5, Cas5d, Cas8c (Csd1), Cas7 (Csd2), Cas10d (Csc3), Csc2, Csc1, Cas6d, Cse1 (CasA), Cse2 (CasB), Cas7 (CasC), Cas5 (CasD), Cas6e (CasE), Cys1, Cys2, Cas7 (Cys3), Cas6f (Csy4), Cas6 and/or Cas4

Type I CRISPR-Cas systems are well known in the art and include, for example, Archaeoglobus fulgidus comprises an exemplary Type I-A CRISPR-Cas system, Clostridium kluyveri DSM 555 comprises an exemplary Type I-B CRISPR-Cas system, Bacillus halodurans C-125 comprises an exemplary Type I-C CRISPR-Cas system, Cyanothece sp. PCC 802 comprises an exemplary Type I-D CRISPR-Cas system, Escherichia coli K-12 comprises an exemplary Type I-E CRISPR-Cas system, Geobacter sulfurreducens comprises an exemplary Type I-U CRISPR-Cas system and Yersinia pseudotuberculosis YPIII comprises an exemplary Type I-F CRISPR-Cas system.

In some embodiments, a Type II polypeptide useful with this invention comprises at least 70% identity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to an amino acid sequence of a Cas9. Type II CRISPR-Cas systems well known in the art and include, for example, Legionella pneumophila str. Paris, Streptococcus thermophilus CNRZ1066 and Neisseria lactamica 020-06.

In some embodiments, a Type III polypeptide useful with this invention comprises at least 70% identity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to an amino acid sequence of a Cas6, Cas10 (or Csm1), Csm2, Csm3, Csm4, Csm5, and Csm6, Cmr1, Cas10 (or Cmr2), Cmr3, Cmr4, Cmr5, and Cmr6, Cas7, Cas10, Cas7 (Csm3), Cas5 (Csm4), Cas7 (Csm5), Csm6, Cas7 (Cmr1), Cas5 (Cmr3), Cas7 (Cmr4), Cas7 (Cmr6), Cas7 (Cmr6), Cmr5, Cas5 (Cmr3), Cas5 (Csx10), Csm2, Cas7 (Csm3), and all1473. Type III CRISPR-Cas systems are well known in the art and include, for example, Staphylococcus epidermidis RP62A, which comprises an exemplary Type III-A CRISPR-Cas system, Pyrococcus furiosus DSM 3638, which comprises an exemplary Type III-B CRISPR-Cas system, Methanothermobacter thermautotrophicus str. Delta H, which comprises an exemplary Type III-C CRISPR-Cas system, and Roseiflexis sp. Rs-1, which comprises an exemplary Type III-D CRISPR-Cas system.

In some embodiments, a Type IV polypeptide useful with this invention comprises at least 70% identity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to an amino acid sequence of a Csf4 (dinG), Csf1, Cas7 (Csf2) and/or Cas5 (csf3). Type IV CRISPR-Cas systems are well known in the art, for example, Acidithiobacillus ferrooxidans ATCC 23270 comprises an exemplary Type IV CRISPR-Cas system.

In some embodiments, a Type V polypeptide useful with this invention comprises at least 70% identity (e.g., about 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and the like) to an amino acid sequence of a Cpf1, Cas1, Cas2, or Cas4. Type V CRISPR-Cas systems are well known in the art and include, for example, Francisella cf. novicida Fx1 comprises an exemplary Type V CRISPR-Cas system.

Additionally provided herein are expression cassettes and vectors comprising the nucleic acid constructs, the nucleic acid arrays, nucleic acid molecules and/or the nucleotide sequences of this invention, which can be used with the methods of this disclosure.

In further aspects, the nucleic acid constructs, nucleic acid arrays, nucleic acid molecules, and/or nucleotide sequences of this invention can be introduced into a cell of a host organism. Any cell/host organism for which this invention is useful with can be used. Exemplary host organisms include bacteria, archaea, algae and fungi (e.g., yeast).

The invention will now be described with reference to the following examples. It should be appreciated that these examples are not intended to limit the scope of the claims to the invention, but are rather intended to be exemplary of certain embodiments. Any variations in the exemplified methods that occur to the skilled artisan are intended to fall within the scope of the invention.

EXAMPLES Example 1. Bacterial Strains

All bacterial strains are listed in Table 1. Bacterial cultures were cryopreserved in an appropriate growth medium with 25% glycerol (vol/vol) and stored at −80° C. S. thermophilus was propagated in Elliker media (Difco) supplemented with 1% beef extract (wt/vol) and 1.9% (wt/vol) β-glycerolphosphate (Sigma) broth under static aerobic conditions at 37° C., or on solid medium with 1.5% (wt/vol) agar (Difco), incubated anaerobically at 37° C. for 48 hours. Concentrations of 2 μg/mL of erythromycin (Em) and 5 μg/mL of chloramphenicol (Cm) (Sigma) were used for plasmid selection in S. thermophilus, when appropriate. E. coli EC1000 was propagated aerobically in Luria-Bertani (Difco) broth at 37° C., or on brain-heart infusion (BHI) (Difco) solid medium supplemented with 1.5% agar. Antibiotic selection of E. coli was maintained with 40 μg/mL kanamycin (Kn) and 150 μg/mL of Em for recombinant E. coli, when appropriate. Screening of S. thermophilus derivatives for β-galactosidase activity was assessed qualitatively by supplementing a synthetic Elliker medium with 1% lactose, 1.5% agar, and 0.04% bromo-cresol purple as a pH indicator.

Example 2. DNA Isolation and Cloning

All kits, enzymes, and reagents were used according to the manufacturers' instructions. DNA purification and cloning were performed as described previously (41). Briefly, purification of genomic DNA from S. thermophilus employed a ZR Fungal/Bacterial MiniPrep kit (Zymo). Plasmid DNA was isolated from E. coli using Qiagen Spin miniprep kit (Qiagen). High fidelity PCR amplification of DNA was performed with PFU HS II DNA polymerase (Stratagene). Routine PCRs were conducted with Choice-Taq Blue polymerase (Denville). Primers for PCR amplification were purchased from Integrated DNA Technologies (Coralville, Iowa). DNA extraction from agarose gels was performed with a Zymoclean DNA gel recovery kit (Zymo). Restriction endonucleases were acquired from Roche Molecular Biochemicals. Ligations were performed with New England Biolabs quick T4 ligase. Sequencing was performed by Davis Sequencing Inc. (Davis, Calif.). Cryopreserved rubidium chloride competent E. coli cells were prepared as previously described (41). Plasmids with lacZ targeting arrays were constructed with each consisting sequentially of the (1) native leader sequence specific to SthCRISPR1 or SthCRISPR3 (2) native repeats specific to CRISPR 1 or CRISPR 3 (3) spacer sequence specific to the 5′ end of lacZ (4) another native repeat (FIG. 1). In order to engineer each plasmid, the sequence features listed above were ordered as extended oligomers (Table 2), combined using splicing by overlap extension PCR (42) and cloned into pORI28 (FIG. 2).

Example 3. Selection and Design of CRISPR Spacers

The programmable specificity of chromosomal cleavage hinges upon selection of a desired spacer sequence unique to the target allele. Specificity is further compounded by the requisite PAM, a short conserved sequence that must be proximate to the proto-spacer in the target sequence (21, 43). Thus, strict criteria for selection and design of spacers were the location of consensus PAM sequences and incidental sequence identity to extraneous genomic loci. Putative protospacers were constrained by first defining the location of all putative PAM sequences in the sense and antisense strands of lacZ. Within the 3,081 nt gene, there were 22 CRISPR1 (AGAAW) and 39 CRISPR3 (GGNG) PAM sites that were identical to their bioinformatically derived consensus sequences (21). After potential spacers were identified, the complete proto-spacer, seed, and PAM sequence were subjected to BLAST analysis against the genome of S. thermophilus LMD-9 to prevent additional targeting of non-specific loci. The spacers for CRISPR1 and CRISPR3 were disparate in sequence and corresponding PAM sites, but were designed to target the 5′ end of lacZ, resulting in predicted cleavage sites residing 6 nt apart. Therefore, the leader sequences, repeats, and spacers on each plasmid represented orthogonal features unique to CRISPR1 or CRISPR3, respectively. To assess target locus-dependent mutations, an additional CRISPR3 plasmid was created with a spacer to the metal cation-binding residue essential for β-galactosidase activity. A CRISPR1 array plasmid containing a non-self-spacer was used as a control to quantify lethality of self-targeting.

Example 4. Transformation

Plasmids were electroporated into competent S. thermophilus containing the temperature-sensitive helper plasmid, pTRK669, according to methods described previously (44). Briefly, an overnight culture of S. thermophilus was inoculated at 1% (vol/vol) into 50 mL of Elliker medium supplemented with 1% beef extract, 1.9% β-glycerophosphate and Cm selection. When the culture achieved an OD₆₀₀ nm of 0.3, penicillin G was added to achieve a final concentration of 10 μg/mL, in order to promote electroporation efficiency (45). Cells were harvested by centrifugation and washed 3× in 10 mL cold electroporation buffer (1 M sucrose and 3.5 mM MgCl₂). The cells were concentrated 100-fold in electroporation buffer and 40 μL of the suspension was aliquoted into 0.1 mm electroporation cuvettes. Each suspension was combined with 700 ng of plasmid. Electroporation conditions were set at 2,500 V, 25 μFd capacitance, and 200 Ohms resistance. Time constants were recorded and ranged from 4.4 to 4.6 ms. The suspensions were immediately combined with 950 μL of recovery medium and incubated for 8 hours at 37° C. Cell suspensions were plated on selective medium and electroporation cuvettes were washed with medium to ensure recovery of cells.

Example 5. β-Galactosidase Phenotype Confirmation

Transformants generated from both CRISPR1 and CRISPR3 were initially screened for the β-galactosidase deficient phenotype by restreaking colonies on semi-synthetic Elliker medium supplemented with 1% lactose as the sold carbohydrate source. Loss of β-galactosidase activity was confirmed by performing Miller assays (o-nitrophenyl-β-D-galactoside (ONPG) (46). Briefly, cultures were propagated to late-log phase (OD₆₀₀ nm of 1.2) in 5 mL of medium and harvested by centrifugation (4,000×g for 10 min). Cells were washed and resuspended in 0.5 mL phosphate-buffered saline (Gibco-Invitrogen). Each suspension was combined with 100 uL of 0.1 mm glass beads (Biospec) and then subjected to five 60 s cycles of homogenization in a Mini-Beadbeater (Biospec). Samples were then centrifuged (15,000×g for 5 min) to remove debris and intact cells. Cell lysates (10 μL aliquots) were combined with 600 μL of substrate solution (60 mM Na₂HPO₄; 40 mM NaH₂PO₄; 1 mg/mL ONPG; 2.7 μL/mL (3-mercaptoethanol) and incubated for 5 min at room temperature, at which point 700 μL stop solution was added (1 M NaCO₃). The absorbance at 420 nm was recorded and activity of β-galactosidase was reported as Miller units, calculated as previously described (46).

Example 6. Growth and Activity Assessment

Cultures were preconditioned for growth assays by subculturing for 12 generations in a semi-synthethic Elliker medium deficient in lactose. Fresh medium was inoculated with an overnight culture at 1% (vol/vol) and incubated at 37° C. statically. OD₆₀₀ monitored hourly until the cultures achieved stationary phase. Acidification of milk was assessed by inoculating skim milk with an overnight culture to a level of 10⁸ cfu/mL and incubating at 42° C. The pH was subsequently monitored using a Mettler Toledo Seven Easy pH meter and Accumet probe. Skim milk was acquired from the NCSU Dairy plant and Pasteurized for 30 min at 80° C.

Example 7. Identification of Expendable Genomic Regions

In silico prediction of mobile and expendable loci for CRISPR-Cas targeting was performed on the basis of i) location, orientation, and nucleotide identity of IS elements, and ii) location of essential ORFs. In Bacillus subtilis, 271 essential ORFs were identified by determining the lethality of genome-wide gene knockouts (33). The S. thermophilus genome was queried for homologues to each essential gene from B. subtilis using the BLASTp search tool under the default scoring matrix for amino acid sequences. Homologues to about 239 essential ORFs were identified in S. thermophilus, all of which were chromosomally encoded (Table 4). Proteins involved in conserved cellular processes including DNA replication/homeostasis, translation machinery, and core metabolic pathways were readily identified. No homologues corresponding to cytochrome biosynthesis/respiration were observed, in accordance with the metabolic profile of fermentative bacteria. Each putative essential ORF was mapped to the reference genome using SnapGene software, facilitating visualization of their location and distribution in S. thermophilus LMD-9 (FIG. 3A).

IS elements within the S. thermophilus genome were grouped by aligning transposon coding sequences using Geneious® software (FIG. 4). Family designations were determined according to BLAST analysis within the IS element database (www-is.biotoul.fr//). To predict the potential for recombination-mediated excision of chromosomal segments, the relative location of related IS elements were mapped to the S. thermophilus genome (FIG. 3A). The IS1193 and Sth6 families of IS elements appeared most frequently in the genome and are commonly found in Streptococcus pneumoniae and Streptococcus mutans (34). Despite the prevalence of IS1193 elements, many of these loci were shown to be small fragments that exhibited some polymorphism and degeneracy, but there were also several copies present with a high level of sequence identity (FIG. 5A). In contrast, the Sth6 family exhibited considerable polymorphism and high degeneracy, with some copies harboring significant internal deletions (FIG. 5B). IS1167 and IS1191 elements were less frequent but exhibited near perfect fidelity between the copies identified in the genome (FIGS. 5C and 5D). Based on the conservation of length and sequence of the IS1167 and IS1191 elements of S. thermophilus, and their relative proximity to milk adaptation genes, we postulate that these conserved/high fidelity transposons were recently acquired in the genome.

By combining the location of predicted essential ORFs and IS elements, expendable islands flanked by IS elements of high fidelity were identified (FIG. 3A) (Table 3). The first island contained an operon unique to S. thermophilus LMD-9, encoding a putative ATP-dependent oligonucleotide transport system with unknown specificity (FIG. 3B) (35). The second harbors the cell-envelope proteinase PrtS which contributes to the fast-acidification phenotype of S. thermophilus (FIG. 3B)(36). Notably, while prtS is not ubiquitous in S. thermophilus genomes, it has been demonstrated that the genomic island encoding prtS is transferable between strains using natural competence (36). The third island contains a putative ATP-dependent copper efflux protein and is present in every sequenced S. thermophilus strain (FIG. 3B). The fourth island is the largest by far in terms of length at 102 kbp, and gene content, with 102 predicted ORFs including the lac operon (FIG. 3B). This island is found in all strains of S. thermophilus, but the specific gene content and length varies among strains. In order to determine the outcome of targeting a large genomic island with both endogenous Type II systems, repeat-spacer arrays were generated for the lacZ coding sequence (FIG. 3B) and cloned into pORI28 (FIG. 2). The fourth island was selected for CRISPR-Cas targeting due to its size, ubiquity in S. thermophilus strains, and the ability to screen for lacZ mutations on the basis of a β-galactosidase negative phenotype.

Example 8. CRISPR-Cas Targeting of lacZ Selects for Large Deletion Events

In Type II systems, Cas9 interrogates DNA and binds reversibly to PAM sequences with activation of Cas9 at the target occurring via formation of the tracrRNA::crRNA duplex (37), ultimately resulting in dsDNA cleavage (FIGS. 6A and 6B)(25). FIGS. 14A and 14B are schematics showing the general approach for co-opting endogenous CRISPR systems for targeted killing. In particular, these FIGS. 14A and 14B show the approach for co-opting endogenous type II systems in Streptococcus thermophilus for targeted killing. Thus, in S. thermophilus, programmed cell death was achieved using the CRISPR-Sth1 (A) or CRISPR-Sth3 (B) Type II system, by designing a genome targeting spacer sequence flanked by native repeats, whose expression was driven by a native or synthetic promoter. The transcribed repeat-spacer array is processed via host encoded RNAase III and Cas9 to yield mature crRNAs, which recruit Cas9 to the genome to elicit double-stranded DNA cleavage resulting in cell death.

Transformation with plasmids eliciting chromosomal self-targeting by CRISPR-Cas systems appeared cytotoxic as measured by the relative reduction in surviving transformants compared to non-self-targeting plasmids (15, 29). Targeting the lacZ gene in S. thermophilus resulted in about a 2.5-log reduction in recovered transformants (FIG. 6C), approaching the limits of transformation efficiency. Double-stranded DNA breaks (DSBs) constitute a significant threat to the survival of organisms. The corresponding repair pathways often require end resection to repair blunt-ended DNA. Cas9-effected endonucleolysis further exacerbates the pressure for mutations caused by DSBs to occur, as restoration of the target locus to the wild-type does not circumvent subsequent CRISPR targeting. Identification of spacer origins within lactic acid bacteria revealed that 22% of spacers exhibit complementarity to self and that the corresponding genomic loci were altered, likely facilitating survival of naturally occurring self-targeting events (28).

To determine if the target locus was mutated in response to Cas9-induced cleavage, transformants were first screened for loss of β-galactosidase activity. Clones deficient in activity were genotyped at the lacZ locus. No mutations due to classical or alternative end joining, nor any spontaneous single nucleotide polymorphisms were observed in any of the clones sequenced. The absence of single nucleotide polymorphisms may be attributed to a low transformation efficiency compounded by low incidence of point mutations, and the absence of Ku and LigaseIV homologs correlated with an absence of non-homologous end joining (38). PCR screening indicated that the wild-type lacZ was not present, but the PCR amplicons did not correspond to the native lacZ locus; rather, an IS element-flanked sequence at another genomic locus was amplified. To investigate the genotype responsible for the loss of β-galactosidase activity, Single Molecule Real Time sequencing was performed on two clones; one generated from CRISPR3 targeting the 5′ end of lacZ, and one generated from CRISPR3 targeting the sequence encoding the ion-binding pocket necessary for (3-galactosidase catalysis (FIG. 7A). This sequencing strategy was employed for its long read length to circumvent difficulty in reliably mapping reads to the proper locus, due to the high number of IS elements in the genome (35). Reads were mapped to the reference genome sequence using Geneious software, and revealed the absence of a large segment (about 102 kbp) encoding the lacZ open reading frame (FIG. 7A). Both sequenced strains confirmed the reproducibility of the large deletion boundaries, and showed that the deletion occurred independently of the lacZ spacer sequence or CRISPR-Cas system used for targeting. However, the sequencing data did not reliably display the precise junctions of the deletion.

The 102 kbp segments deleted constitute approximately 5.5% of the 1.86 Mbp genome of S. thermophilus. The region contained 102 putative ORFs (STER_1278-1379), encoding ABC transporters, two-component regulatory systems, bacteriocin synthesis genes, phage related proteins, lactose catabolism genes, and several cryptic genes with no annotated function (35). The effect of the deletion on growth phenotype was assessed in broth culture by measuring OD 600 nm over time (FIG. 7B). The deletion clones appeared to have a longer lag phase, lower final OD (p<0.01) and exhibited a significantly longer generation time during log phase with an average of 103 min, compared to 62 min for the wild-type (p<0.001). Although the deletion derivatives have 5.5% less of the genome to replicate per generation, and expend no resources in transcription or translation of the eliminated ORFs, no apparent increase in fitness was observed relative to the wild-type. β-galactosidase activity is a hallmark feature for industrial application of lactic acid bacteria and is essential for preservation of food systems through acidification. The capacity of lacZ deficient S. thermophilus strains to acidify milk was therefore assessed by monitoring pH (FIG. 7B). Predictably, the deletion strain failed to acidify milk over the course of the experiment, in sharp contrast to the rapid acidification phenotype observed in the wild-type.

Example 9. Genomic Deletions Occur Through Recombination Between Homologous IS Elements

In order to investigate the mechanism of deletion, the nucleotide sequences flanking the segment were determined. The only homologous sequences observed at the junctions were two truncated IS1193 insertion sequences exhibiting 91% nucleotide sequence identity globally over 727 bp. Accordingly, a primer pair flanking the two IS elements was designed to amplify genomic DNA of surviving clones exhibiting the deletion. Each of the deletion strains exhibited a strong band of the predicted size (about 1.2 kb), and confirmed the large genomic deletion event (FIG. 8, top left panel). Interestingly, a faint amplicon corresponding to the chromosomal deletion was observed in the wild-type, indicating that this region may naturally excise from the genome at a low rate within wild-type populations. Sequencing of the junction amplicon was performed for 20 clones generated by chromosomal self-targeting by CRISPR3. Genotyping of the locus revealed the presence of one chimeric IS element in each clone and, furthermore, revealed the transition from the upstream element to the downstream sequence within the chimera for each clone (FIG. 8, top middle panel). The size of deletions observed ranged from 101,865-102,146 bp. The exact locus of transition was variable, but non-random within the clones, implying the potential bias of the deletion mechanism. S. thermophilus harbors typical recombination machinery encoded as RecA (STER_0077), AddAB homologs functioning as dual ATP-dependent DNA exonucleases (STER_1681 and STER_1682), and a helicase (STER_1742) of the RecD family. The high nucleotide identity between the flanking IS elements and the capacity for S. thermophilus to carry out site-specific recombination (4) confirms the potential for RecA-mediated recombination to mediate excision of the genomic segment (FIG. 8, top right panel).

Next, CRISPR-Cas targeting was evaluated for the ability to facilitate isolation of deletions for each locus with the same genetic architecture. For this purpose, three CRISPR3 repeat-spacer arrays, one targeting the oligonucleotide transporter in the first locus, prtS from the second locus, and the ATPase copper efflux gene from the third locus were generated and cloned into pORI28 (FIG. 5). In order to screen for deletions, primers flanking the IS elements at each locus were designed to amplify each deletion junction (FIG. 8, bottom left panel). The absence of wild-type loci was also confirmed in each case by designing internal primers for each genomic island (FIG. 8, bottom right panel) Following transformations with the targeting plasmids, deletions at each locus were isolated and the absence of wild-type confirmed. Sequencing of the deletion junction amplicons confirmed that a single chimeric IS element footprint remained, indicating a common mechanism for deletion at each locus. Interestingly, primers flanking the IS elements also amplified from wild-type gDNA, further suggesting that population heterogeneity naturally occurred at each locus was due to spontaneous genomic deletions. These results imply that sequence-specific Cas9 cleavage selects for the variants lacking protospacer and PAM combinations necessary for targeting. Thus, spontaneous genomic deletions can be isolated using CRISPR-Cas targeting as a strong selection for microbial variants that have already lost those genomic islands.

Example 10. Population Screening

In this study, native Type IIA systems harbored in S. thermophilus were repurposed for defining spontaneous deletions of large genomic islands. By independently targeting four islands in S. thermophilus, stable mutants collectively lacking a total of 7% of the genome were generated. Characterization of the deletion junctions suggested that an IS-dependent recombination mechanism contributes to population heterogeneity and revealed deletion events ranging from 8 to 102 kbp. Precise mapping of the chimeric IS elements indicated that natural recombination events are likely responsible for the large chromosomal deletions in S. thermophilus and could potentially be exploited for targeted genome editing.

Our results demonstrate that wild-type clones were removed from the population while mutants without CRISPR-Cas targeted features survived. Thus, adaptive islands were identified and validated, showing that precise targeting by an endogenous Cas9 can be exploited for isolating large deletion variants in mixed populations.

Genome evolution of bacteria occurs through horizontal gene transfer, intrinsic mutation, and genome restructuring. Genome sequencing and comparative analysis of S. thermophilus strains has revealed significant genome decay, but also indicates that adaptation to nutrient-rich food environments occurred through niche-specific gene acquisition (18; 35). The presence of MGEs including integrative and conjugative elements, prophages, and IS elements in S. thermophilus genomes is indicative of rapid evolution to a dairy environment (38-39). Mobile genetic features facilitate gene acquisition and conversely, inactivation or loss of non-essential sequences. Consequently, MGEs confer genomic plasticity as a means of increasing fitness or changing ecological lifestyles. Our results strongly indicate that CRISPR-Cas targeting of these elements may influence chromosomal rearrangements and homeostasis. This is in contrast to experiments targeting essential features, which resulted in selection of variants with inactivated CRISPR-Cas machinery (Jiang 2013). Mutation of essential ORFs is not a viable avenue for circumvention of CRISPR-Cas targeting, and thus only those clones with inactivated CRISPR-Cas systems remain. By design, targeting genetic elements predicted to be hypervariable and expendable demonstrated that variants with altered loci were viable, maintaining active CRISPR-Cas systems during self-targeting events.

Despite the near ubiquitous distribution of IS elements in bacterial genomes they remain an enigmatic genetic entity, largely due to their diversity and plasticity in function (34). Our results suggest it is possible to predict recombination between related IS elements by analyzing their location, orientation, and sequence conservation (FIG. 4 and FIGS. 5A-5D). CRISPR-Cas targeting can then be employed to empirically validate population heterogeneity at each predicted locus, and simultaneously increase the recovery of low incidence mutants. The high prevalence of MGEs in lactic acid bacteria, and especially S. thermophilus, is in accordance with their role in speciation of these hyper-adapted bacteria through genome evolution (39-40). Moreover, recovery of genomic deletion mutants using CRISPR-Cas targeting could facilitate phenotypic characterization of genes with unknown function. Mutants exhibiting the deletion of the 102 kb island encoding the lac operon had significantly increased generation times relative to the wild-type and achieved a lower final OD. With 102 predicted ORFs therein, it is likely that additional phenotypes are affected and many of the genes do not have annotated functions. Considering the industrial relevance of niche-specific genes such as prtS, this method allows for direct assessment of how island-encoded genes contribute to adaption to grow in milk. Moreover, it is in the natural genomic and ecological context of these horizontally acquired traits, since they were likely acquired as discrete islands. These results establish new avenues for the application of self-targeting CRISPR-Cas9 systems in bacteria for investigation of transposition, DNA repair mechanisms, and genome plasticity.

CRISPR-Cas systems generally limit genetic diversity through interference with genetic elements, but acquired MGEs can also provide adaptive advantages to host bacteria. Thus, the benefit of maintaining genomically integrated MGEs despite CRISPR-Cas targeting is an important driver of genome homeostasis. Collectively, our results establish that in sit/co prediction of GEIs can be coupled with CRISPR-Cas targeting to isolate clones exhibiting large genomic deletions. Chimeric insertion sequence footprints at each deletion junction indicated a common mechanism of deletion for all four islands. The high prevalence of self-targeting spacers exhibiting identity to genomic loci, combined with experimental demonstrations of genomic alterations, suggest that CRISPR-Cas self-targeting may contribute significantly to genome evolution of bacteria (28;30). Collectively, studies on CRISPR-Cas induced large deletions substantiate this approach as a rapid and effective means to assess the essentiality and functionality of gene clusters devoid of annotation, and define minimal bacterial genomes based on chromosomal deletions occurring through transposable elements.

FIG. 9 shows defined genetic loci for assessing type II CRISPR-Cas system-based lethality via targeting the genome of Streptococcus thermophilus LMD-9. The methods to carry out this analysis are known in the art. See, Selle and Barrangou PNAS. 112(26):8076-8081 (2015).

Both orthogonal type II systems (CRISPR1 and CRISPR3) were tested; CRISPR1 targets in dark grey, CRISPR3 targets in light grey. Specific genetic features were selected to test (i) intergenic regions (INT), (ii) mobile genetic elements (IS, GEI1-GEI3, PRO, lacZ, EPS), (iii) essential genes (dltA, LTA), (iv) poles of the replichore (ORI, TER), and forward versus reverse strands of DNA (outer targets versus inner targets).

FIG. 10 shows CRISPR-based lethality achieved by targeting the regions defined in FIG. 9. Log reduction in CFU was calculated with regard to transformation of a non-targeting plasmid control; pORI28. Lethality ranged from 2-3 log reduction for all targets tested, regardless of chromosomal location, coding sequence, or essentiality.

FIG. 11 shows transcriptional profiles of CRISPR-mediated genomic island deletion strains. Recovery and genotyping of cells surviving CRISPR targeting of the genomic islands 1-4 resulted in identification of stable independent mutants lacking the genomic island targeted in each experiment. Subsequently, the cells were propagated and their total RNA was isolated and sequenced. Using this approach, transcriptional profiles were generated by mapping sequencing reads to the reference genome. In each case, the absence of sequencing reads to the predicted genomic island loci further suggested the loss of the target genetic entity, while having minimal impact on the expression of core genes throughout the rest of the genome.

Furthermore, RNA sequencing data supports the boundaries of the deletions by using read coverage mapping and transcriptional value comparisons and additionally supports the discernment of phenotype using comparative transcriptomics generated using the same data set. Specifically, the lack of transcriptional activity present at the expected deletion regions using high-throughput RNA-sequencing is confirmed as shown in FIG. 12. FIG. 12 shows log₂ transformed RNA-sequencing read coverage of genomic island deletion strains and for each genomic island strain (GEI1-GEI4), the absence of sequencing reads to the predicted genomic island loci further suggested the loss of the target genetic entity, while having minimal impact on the expression of core genes throughout the rest of the genome.

FIG. 13 further confirms lack of transcriptional activity for the deleted genes. For each of the genomic island deletion strains (GEI1-GEI4), the expression of genes encoded on each of the target islands (black) was minimal. Genes encoded in GEI1 are shown in the upper left panel, genes encoded in GEI2 are shown in the upper right panel, genes encoded in GEI3 are shown in the lower left panel, and genes encoded in GEI4 are shown in the lower right panel. In general, genomic island deletions 1 and 2 had minimal impact on the transcription of other genes (gray), whereas genomic island 3 and 4 appeared to affect the transcription of other genes not encoded on the islands.

In addition, RNA-sequencing data was used to compare the transcriptional levels of genes not encoded on the deleted island (GEI4), i.e., other genes still present in the chromosome, and identifying phenotypes associated with genomic deletions. Genes that are differentially transcribed in the deletion strain suggest that cellular processes were impacted by the genes that were lost or that there is compensation for the loss of the activity of these genes. Thus, inferences can be made about the pathways to which these genes or genomic regions are relevant. Table 5 provides a list of differentially expressed genes identified in deletion strain GEI4. Many of the genes observed to be differentially expressed relate to the biosynthetic capacity of Streptococcus thermophilus, including aromatic amino acid and purine biosynthesis.

Example 11. Targeted Killing of Lactobacillus casei Using a Type II CRISPR-Cas System

Exemplary CRISPR-Cas Type II guides of L. Casei are provided in FIG. 15. The first structure provides a predicted guide, while the second structure shows an exemplary dual guide structure and the third structure shows an exemplary single guide structure.

Example 12. Targeted Killing of Lactobacillus gasseri Using a Type II CRISPR-Cas System

Exemplary Type II guides for targeted killing of L. gasseri are provided in FIG. 16. The first structure provides the predicted guide, while the second structure provides the correct dual guide crRNA:tracrRNA (confirmed by RNA sequencing) and the third structure provides an exemplary predicted single guide.

Plasmids were transformed into L. gasseri each carrying different constructs as follows: an empty pTRK563 vector, a construct with the correct protospacer but an incorrect PAM, the correct PAM but a protospacer that is not in the array, and the correct protospacer with the PAM. The results are shown in FIG. 19. The plasmid having the correct protospacer and correct PAM showed significantly more interference targeting and cell death.

Example 13. Targeted Killing of Lactobacillus pentosus Using a Type II CRISPR-Cas System

Exemplary Type II guides for targeted killing of L. pentosus are provided in FIG. 17. The first structure shows the predicted guide. The second structure is the correct dual guide crRNA:tracrRNA (confirmed by RNA Sequencing) and the third structure is an exemplary predicted artificial single guide.

Plasmids were transformed into L. pentosus, each plasmid carrying different constructs as follows: a construct with the correct protospacer but an incorrect PAM, a construct with a correct PAM but a protospacer that is not in the array, an empty pTRK563 vector, and a correct protospacer with a correct PAM. The results are shown in FIG. 20. The plasmid having a correct protospacer and correct PAM (Lpe1 gttaat) showed significantly more interference targeting and cell death.

Example 14. Targeted Killing of Lactobacillus jensenii Using a Type II CRISPR-Cas System

FIG. 18 provides exemplary CRISPR-Cas Type II guides. The first structure is the correct dual guide crRNA:tracrRNA as confirmed by RNA sequencing and the second structure is an exemplary predicted artificial single guide.

Plasmids were transformed into L. jensenii each carrying different constructs as follows: a construct comprising an empty pTRK563 vector, a construct with the correct protospacer but an incorrect PAM, a construct with a correct PAM but a protospacer that is not in the array, and a construct having a correct protospacer with a correct PAM. The results are shown in FIG. 22. The plasmid having a correct protospacer and correct PAM showed substantially more interference targeting and cell death.

Example 15. Targeted Killing of Lactobacillus casei NCK 125 Using a Type I CRISPR-Cas System

FIG. 21 provides an exemplary Type I CRISPR-Cas guide for L. casei, which comprises the sequence of the native Type I leader and repeat found in L. casei NCK 125. PAM 5′-YAA-3′ was predicted using the native spacer sequences in the organism. The artificial array contains a spacer that targets the 16s rDNA gene in the host genome. The results are provided in FIG. 22, which shows a significant reduction between the empty vector and two different artificial arrays: one of which contains a single spacer targeting the + strand in the 16s gene (1-2 alt) and the other containing the original spacer targeting the + strand but containing an additional spacer targeting the − strand in the 16s gene (1, 2-3).

CRISPR-Cas systems as described herein may be used for, for example, (i) targeted reduction of pathogens in the case of either medical intervention (e.g., pathogens including but not limited to, fungi, nematodes, protozoa (e.g., malaria), cestodes, coccidia (microsporidia), trematodes, pentastomids, acanthocephalans, arthropods, and the like); (ii) for protection of consumables (food systems, animals, crops); (iii) for control and/or removal of undesirable organisms from industrial fermentative processes (raw materials, processing equipment, starter cultures) and (iv) for control of environmental microbial consortia to impact ecosystems and/or chemical cycles as well as for remediation.

TABLE 1 Bacterial Strains and Plasmids Strain Original designation Description Reference E. coli EC1000 Host for pORI plasmids, chromosomal 47 repA⁺ (pWVO1), Km^(R) Host for pTRK935 S. thermophilus Wild-type 40 LMD-9 Wild-type, RepA⁺ and Cm^(R) This study S thermophilus conferred by pTRK669 LMD-9 with pTRK669 Plasmids pORI28 Broad range non-replicative vector, Em^(R) 47 pTRK669 Ts-helper plasmid repA⁺ , Cm^(R) 44 pCRISPR1::lacZ pORI28::CRISPR1-Leader-RSR-lacZ This study N-terminus spacer pCRISPR3::lacZ pORI28::CRISPR1-Leader-RSR-lacZ This study active site spacer pCRISPR3::ABC pORI28::CRISPR1-Leader- This study RSR-ABC spacer pCRISPR3::Cu pORI28::CRISPR1-Leader-RSR-Cu This study efflux spacer pCRISPR3::prts pORI28::CRISPR1-Leader- This study RSR-prts spacer pCRISPR3::lacZ pORI28::CRISPR3-Leader-RSR-lacZ This study N-terminus spacer pCRISPR1::Non- pORI28::CRISPR1-Leader-RSR- This study self non self spacer

TABLE 2 Primers Primer Name Sequence Function C1_N-term_F CAAGAACAGTTATTGATTTTATAATCACTATGTGGGTATGAAAATCTCAAAAATCATTTGAGGTTTT Template for SOE-PCR TGTACTCTCAAGATTTAAGTAACTGTACAACATTAAGAGATTGTCTTAACTT SEQ ID NO: 51 C3_N-term AGCGGATAACAATTTCACGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACTCAGAAAATTCTT Template for SOE-PCR CAAGAGATTCAAAATACTGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACCTCGTAGGATATC TTTTCTAC SEQ ID NO: 52 Cl _N-term_R AGCGGATAACAATTTCACGTTGTACAGTTACTTAAATCTTGAGAGTACAAAAACAGGGGAGATGAAG Template for SOE-PCR TTAAGACAATCTCTTAATGT SEQ ID NO: 53 C3_A-site AGCGGATAACAATTTCACGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACGAAGTCTTGGTCT Template for SOE-PCR TCCAACCAGCTTGCTGTAGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACCTCGTAGGATATC TTTTCTAC SEQ ID NO: 54 C3_ABC AGCGGATAACAATTTCACGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACGATAACACGAGAT AAAACATCCAGCCCACCGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACctcgtaggatatct tttctac SEQ ID NO: 55 C3_prtS AGCGGATAACAATTTCACGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACGTTGTAGCTTTGA GGTCTGAGAATACACGCGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACctcgtaggatatct tttctac SEQ ID NO: 56 C3_Cu AGCGGATAACAATTTCACGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACGATTGCTCAATCA ATCGTTTCAGCTGCTAAGTTTTGGAACCATTCGAAACAACACAGCTCTAAAACctcgtaggatatct tttctac SEQ ID NO: 57 C3LF AGCAGGGATCCTGGTAATAAGTATAGATAGTCTTG SEQ ID NO: 58 Amplify Sth3 Leader  from gDNA C3LR CTCGTAGGATATCTTTTCTAC SEQ ID NO: 59 Amplify Sth3 Leader  from gDNA C1F AGCAGGGATCCCAAGAACAGTTATTGATTTTATAATC SEQ ID NO: 60 CRISPR1 SOE-PCR  Forward C3F AGCAGGGATCCTGGTAATAAGTATAGATAGTCTTG SEQ ID NO: 61 CRISPR3 SOE-PCR  Foward C1C3R TGCTGGAGCTCGTGAAATTGTTATCCGCT SEQ ID NO: 62 CRISPR1 and CRISPR3  SOE-PCR Reverse 1193F TTGAACACTAGGAACCTCATA SEQ ID NO: 63 Deletion junction  amplification 1193R CGTAAGGTTTTGATGACTCAAG SEQ ID NO: 64 Deletion junction  amplification pORI28F TTGGTTGATAATGAACTGTGCTG SEQ ID NO: 65 Sequencing MCS of  pORI28 pORI28R TTGTTGTTTTTATGATTACAAAGTGA SEQ ID NO: 66 Sequencing MCS of  pORI28

TABLE 3 Putative expendable genomic islands and islets. GC Genomic Length content island ORF region kbp % Notable genes IS family 1 STER_139-STER_148 7.81 37.1 Oligopeptide transporters IS6 2 STER_840-STER_848 10.29 39.9 Proteinase PrtS ISSth16/ IS1167 3 STER_881-STER_888 8.71 39.3 Copper efflux IS1191 4 STER_1277-STER_1380 101.76 37.2 Lactose catabolism, 2- IS1193 component reg., bacteriocin synthesis, ABC transporters

TABLE 4 Homologues to about 239 essential ORFs identified in S. thermophilus. Genome_ query part STER start stop direction cover e-value aa id Bacillus subtilis annotation CSTER 1 101 1465 + chromosomal replication  98% 4.00E−124 44% Chromosomal replication initiation prot. DnaA initiator protein DnaA CSTER 2 1620 2756 + DNA polymerase III  99% 1.00E−88  39% DNA polymerase III subunit beta subunit beta dnan CSTER 6 5818 6387 + Peptidyl-tRNA hydrolase  97% 1.00E−61  51% CSTER 9 10331 10702 + cell-cycle prot.  94% 1.00E−05  22% Cell division protein DivlC CSTER 12 12122 13387 + tRNA(lle)-lysidine  92% 3.00E−40  32% tRNA(lle)-lysidine synthetase, MesJ synthase tils CSTER 13 13469 14011 + Hypoxanthine-guanine  99% 2.00E−82  63% Hypoxanthine-guanine phosphoribosyltransferase phosphoribosyltransferase hprt CSTER 40 25595 26425 + Cell shape-determining  94% 1.00E−22  28% Cell shape-determining protein MreC protein MreC CSTER 43 28617 29582 + ribose-phosphate  97% 3.00E−145 65% Ribose-phosphate pyrophosphokinase pyrophosphokinase prs CSTER 47 32842 33846 + put. glycerol-3-phosphate  94% 9.00E−124 54% Phosphate acyltransferase acyltransferase PlsX CSTER 48 33846 34091 + acyl carrier prot.  76% 1.00E−08  40% Acyl carrier protein CSTER 65 53036 54727 − Arginyl-tRNA synthetase  98% 6.00E−52  28% CSTER 95 72798 77192 + DNA polymerase  99% 0.00E+00  51% DNA polymerase III PolC III PolC-type CSTER 105 82956 83723 + 30S ribosomal prot. S2  96% 1.00E−118 69% CSTER 106 83841 84881 + Translation elongation  97% 8.00E−72  44% factor Ts CSTER 117 97363 98706 + Cysteinyl-tRNA synthetase  99% 1.00E−178 54% CSTER 127 104406 104852 + 50S ribosomal prot. L13  99% 9.00E−57  57% CSTER 128 104880 105272 + 30S ribosomal prot. S9 100% 3.00E−59  68% CSTER 193 159363 160967 + CTP synthetase  99% 0.00E+00  68% CTP synthase pyrg CSTER 199 166439 166897 − conserv. hyp. prot.  81% 2.00E−07  28% Protein Nrdl CSTER 208 176203 176472 + 30S ribosomal prot. S15 100% 6.00E−38  63% CSTER 217 183028 184185 + undecaprenyl  98% 2.00E−68  38% Probable undecaprenyl- pyrophosphate phosphate phosphatase N-acetylglucosaminyl 1-phosphate transferase tagO CSTER 218 184346 185116 + ABC transporter  95% 8.00E−130 71% Vegetative protein ATPase 296 sufC CSTER 219 185153 186415 + hyp. prot.  97% 4.00E−111 42% FeS cluster assembly protein SufD CSTER 220 186469 187701 + put. aminotransferase  98% 0.00E+00  60% Cysteine (class V) desulfurase SufS CSTER 221 187688 188122 + NifU fam. prot.  95% 3.00E−48  51% Zinc-dependent sulfurtransferase SufU CSTER 245 208199 208993 + phosphatidate  98% 3.00E−67  41% Phosphatidate cytidylyltransferase cytidylyltransferase CSTER 247 210343 212205 + Prolyl-tRNA synthetase  98% 0.00E+00  50% CSTER 252 215735 216022 + Co-chaperonin  97% 1.00E−18  43% GroES (HSP10) CSTER 253 216071 217690 + Chaperonin GroEL  98% 0.00E+00  75% (HSP60 family) CSTER 261 224055 224204 + 50S ribosomal prot. L33  97% 9.00E−12  50% CSTER 262 224216 224392 + Preprotein translocase  81% 1.40E+00  21% Protein translocase subunit SecE subunit SecE CSTER 268 227616 230117 + Leucyl-tRNA synthetase  99% 0.00E+00  70% CSTER 273 232342 233796 + nicotinate  97% 0.00E+00  63% Nicotinate phosphoribosyltransferase phosphoribosyltransferase pncb CSTER 274 233808 234629 + NAD synthetase 100% 9.00E−109 59% NH(3)-dependent NAD(+) synthetase nade CSTER 286 248252 249580 + UDP-N-acetylmuramate-  99% 3.00E−170 55% UDP-N-acetylmuramate--L- alanine ligase alanine ligase murC CSTER 302 260849 261664 + Glutamate racemase  94% 7.00E−83  48% Glutamate racemase 1 racE CSTER 307 264328 265041 + segregation and  93% 5.00E−37  39% Segregation and condensation prot. A condensation protein A CSTER 308 265034 265615 + segregation and  94% 9.00E−36  40% Segregation and condensation prot. B condensation protein B CSTER 313 269788 270297 + rRNA methytransferase  96% 3.00E−58  51% rRNA methyltransferase CSTER 349 303983 305959 + Transketolase  98% 0.00E+00  58% Transketolase tkt CSTER 357 312857 314032 + chromosome replication  63% 3.00E−02  18% Replication initiation initiation/membrane and membrane attachment attachment protein protein DnaB CSTER 358 314036 314938 + primosomal prot. Dnal  99% 7.00E−58  35% Primosomal protein Dnal CSTER 359 315044 316354 + GTP-binding prot. EngA 100% 0.00E+00  67% GTPase Der CSTER 368 321054 322394 − Seryl-tRNA synthetase 100% 0.00E+00  63% CSTER 376 329673 330116 + conserved hyp. prot.  89% 6.00E−33  43% tRNA threonylcarbamoyladenosine biosynthesis protein TsaE CSTER 380 332545 333732 + Transcription  90% 2.00E−113 46% Transcription elongation factor termination/ antitermination protein NusA CSTER 383 334363 337194 + Translation initiation  99% 0.00E+00  55% factor IF-2 CSTER 387 339864 341309 − UDP-N-  92% 3.00E−52  29% UDP-N- acetylmuramoylalanyl- acetylmuramoyl-L- D-glutamate--2, alanyl-D-glutamate--2, 6-diaminopimelate 6-diaminopimelate ligase ligase murE CSTER 419 364962 365894 + put. manganese-  99% 3.00E−125 58% Manganese- dependent inorganic dependent inorganic pyrophosphatase pyrophosphatase ppac CSTER 430 375355 375579 + acyl carrier prot.  93% 5.00E−14  49% Acyl carrier protein CSTER 432 376667 377593 + acyl-carrier-protein S-  95% 3.00E−86  47% Malonyl CoA- malonyltransferase acyl carrier protein transacylase CSTER 433 377606 378340 + 3-ketoacyl-(acyl-  99% 6.00E−79  47% 3-oxoacyl-[acyl-carrier- carrier-protein) reductase protein] reductase FabG CSTER 434 378401 379633 + 3-oxoacyl-(acyl  99% 1.00E−133 48% 3-oxoacyl-[acyl-carrier- carrier protein) synthase II protein] synthase 2 CSTER 435 379637 380125 + acetyl-CoA carboxylase  98% 9.00E−26  37% Biotin carboxyl carrier biotin carboxyl carrier protein of acetyl- protein subunit CoA carboxylase CSTER 437 380667 382037 + acetyl-CoA  98% 0.00E+00  60% Biotin carboxylase 1 carboxylase biotin carboxylase subunit CSTER 438 382043 382909 + acetyl-CoA carboxylase  94% 8.00E−98  51% Acetyl-coenzyme subunit beta A carboxylase carboxyl transferase subunit beta CSTER 439 382906 383676 + acetyl-CoA carboxylase  76% 2.00E−81  53% Acetyl-coenzyme subunit alpha A carboxylase carboxyl transferase subunit alpha CSTER 442 385819 387417 + conserved hyp. prot.  98% 0.00E+00  58% Ribonuclease Y ymda CSTER 455 402156 402470 + 50S ribosomal prot. L21  99% 2.00E−44  66% CSTER 456 402507 402797 + 50S ribosomal prot. L27  95% 5.00E−47  79% CSTER 460 405038 405805 + Dihydrodipicolinate  98% 7.00E−95  53% 4-hydroxy- reductase tetrahydrodipicolinate reductase dapb CSTER 461 405802 407010 + tRNA CCA-  98% 6.00E−86  40% CCA-adding enzyme pyrophosphorylase CSTER 475 422256 422813 + Ribosome recycling factor 100% 2.00E−68  56% CSTER 485 430547 432550 + Methyonyl-tRNA synthetase  98% 0.00E+00  58% CSTER 492 438748 439890 + protease maturation  91% 6.00E−11  26% Foldase protein PrsA prot. precursor CSTER 493 440232 442850 + Alanyl-tRNA synthetase  99% 0.00E+00  52% CSTER 513 460453 463104 + Valyl-tRNA synthetase  99% 0.00E+00  63% CSTER 523 469888 471168 + cell division  93% 4.00E−59  34% Putative lipid II prot. FtsW flippase FtsW CSTER 524 471406 472602 + elongation factor Tu  99% 0.00E+00  76% CSTER 525 472851 473609 + Triosephosphate  97% 8.00E−109 62% Triosephosphate isomerase isomerase tpia CSTER 526 473848 474477 + Thymidylate  96% 4.00E−73  55% Thymidylate kinase kinase tmk CSTER 527 474486 475361 + DNA polymerase  96% 8.00E−41  33% DNA polymerase III subunit delta′ III subunit delta′ CSTER 539 484827 485744 + Glycyl-tRNA synthetase,  97% 4.00E−169 74% alpha subunit CSTER 540 486028 488064 + Glycyl-tRNA synthetase,  97% 0.00E+00  45% beta subunit CSTER 567 512413 512916 + 50S ribosomal prot. L10 100% 7.00E−61  57% CSTER 568 512991 513359 + 50S ribosomal prot. L7/L12 100% 4.00E−38  67% CSTER 603 548926 550308 + N-acetylglucosamine-  97% 3.00E−164 52% Bifunctional 1-phosphate protein GlmU uridyltransferase CSTER 623 566278 566781 + Dihydrofolate  94% 8.00E−34  38% Dihydrofolate reductase reductase dfra CSTER 626 568210 568809 + GTPase EngB  96% 7.00E−92  63% Probable GTP- binding protein EngB CSTER 632 573613 574254 − put. glycerol-3-phosphate  90% 3.00E−40  46% Glycerol-3-phosphate acyltransferase PlsY acyltransferase plsy CSTER 633 574392 576341 + DNA topoisomerase  97% 0.00E+00  71% DNA topoisomerase IV subunit B 4 subunit B CSTER 634 576969 579434 + DNA topoisomerase  95% 0.00E+00  54% DNA topoisomerase IV subunit A 4 subunit methylenetetrahydrofolate dehydrogenase/ methenyltetrahydrofolate CSTER 660 598871 599725 + cyclohydrolase  99% 2.00E−109 56% Bifunctional protein FolD CSTER 668 605570 606469 + GTPase Era  98% 5.00E−143 64% GTPase Era CSTER 670 607313 607927 + Dephospho-  95% 2.00E−50  45% Dephospho- CoA kinase CoA kinase coae 672 609192 609338 50S ribosomal prot. L33  97% 1.00E−16  52% CSTER 684 620012 621316 + Enolase 100% 0.00E+00  70% Enolase eno CSTER 731 664470 665690 − put. cytosine-  60% 5.00E−16  31% Probable C5 specific DNA BsuMI modification methylase methylase subunit YdiO CSTER 733 666939 668429 − Lysyl-tRNA  97% 0.00E+00  64% synthetase (class II) CSTER 761 694548 695582 + DNA polymerase  84% 2.00E−37  33% Uncharacterized III delta subunit protein YqeN CSTER 773 704704 706056 + UDP-N-acetylmuramoyl-  98% 8.00E−147 49% UDP-N- L-alanyl-D- acetylmuramoylalanine-- glutamate synthetase D-glutamate ligase murD CSTER 774 706060 707130 + N-acetylglucosaminyl  95% 3.00E−30  27% UDP-N- transferase acetylglucosamine--N- acetylmuramy1- (pentapeptide) pyrophosphoryl- undecaprenol N- acetylglucosamine transferase murG CSTER 775 707140 708264 + Cell division protein FtsQ  79% 4.00E−15  26% Cell division protein DivlB CSTER 776 708388 709764 + Cell division protein FtsA  84% 4.00E−103 44% Cell division protein FtsA CSTER 777 709793 711115 + Cell division protein FtsZ  92% 2.00E−123 53% Cell division protein FtsZ CSTER 783 714803 717592 + Isoleucyl-tRNA synthetase  99% 0.00E+00  58% CSTER 787 720193 720459 − 50S ribosomal protein L31 100% 1.00E−22  50% CSTER 793 725315 726394 + Peptide chain  99% 6.00E−158 59% release factor 1 CSTER 796 727911 729161 + serine  97% 2.00E−171 60% Serine hydroxymethyltransferase hydroxymethyltransferase glya CSTER 833 760678 762396 − put. phosphoglucomutase  98% 0.00E+00  47% Phosphoglucomutase pgm CSTER 850 783500 783736 − 30S ribosomal prot. S20  94% 1.00E−13  46% CSTER 864 797961 799307 + Asparaginyl-  99% 4.00E−180 56% tRNA synthetases CSTER 903 833853 835661 + D-fructose-6-phosphate 100% 0.00E+00  59% Glutamine--fructose- amidotransferase 6-phosphate aminotransferase [isomerizing] glmS CSTER 915 845349 846911 + Signal recognition  95% 2.00E−178 57% Signal recognition particle prot. particle protein CSTER 919 848991 849845 + ribosomal  98% 8.00E−101 50% Ribosome biogenesis biogenesis GTPase GTPase rbga CSTER 923 852605 854749 + DNA topoisomerase I  98% 0.00E+00  64% DNA topoisomerase 1 CSTER 994 915311 917623 + ATP-dependent DNA  99% 0.00E+00  54% ATP-dependent DNA helicase PcrA helicase PcrA CSTER 1034 959843 961231 − branched-chain  99% 5.00E−69  34% Dihydrolipoyllysine- alpha-keto acid residue dehydrogenase succinyltransferase subunit E2 component of 2-oxoglutarate dehydrogenase complex odhb CSTER 1036 962412 963383 − acetoin  81% 3.00E−33  28% Pyruvate dehydrogenase dehydrogenase complex, E1 component E1 component, subunit alpha pdha alpha subunit CSTER 1087 1007529 1007888 − 505 ribosomal prot. L20  85% 2.00E−56  80% CSTER 1088 1007945 1008145 − 505 ribosomal prot. L35 100% 1.00E−23  62% CSTER 1089 1008184 1008714 − Translation initiation  98% 2.00E−63  60% factor 3 (IF-3) CSTER 1102 1017867 1018880 − Peptide chain  91% 2.00E−137 57% release factor 2 CSTER 1115 1029796 1031136 − sensor histidine kinase  97% 4.00E−117 71% Transcriptional regulatory protein YycF CSTER 1116 1031129 1031836 − two-component  68% 2.00E−120 47% Sensor histidine response regulator kinase YycG CSTER 1123 1036555 1037826 − UDP-N-acetylglucosamine  96% 2.00E−172 59% UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1-carboxyvinyltransferase 1 muraa CSTER 1135 1049456 1050649 − S-adenosylmethionine  97% 0.00E+00  67% S-adenosylmethionine synthase synthetase metk CSTER 1136 1050929 1051867 + biotin-(acetyl-CoA  92% 4.00E−44  33% Bifunctional ligase/ carboxylase) ligase repressor BirA CSTER 1138 1052266 1053918 − DNA polymerase III,  93% 3.00E−137 44% DNA polymerase gamma/tau subunit III subunit gamma/tau Dnax CSTER 1144 1056546 1056893 − 505 ribosomal prot. L19 100% 2.00E−61  77% CSTER 1164 1073225 1074244 − 6-phosphofructokinase  93% 4.00E−124 61% ATP-dependent 6- phosphofructokinase pfka CSTER 1165 1074337 1077447 − DNA polymerase III,  96% 0.00E+00  35% DNA polymerase III alpha subunit DnaE subunit alpha dnae CSTER 1166 1077600 1078385 − Putative translation  42% 3.00E−04  24% ywlC unknown factor (SUA5) conserved protein with a putative RNA binding motif TW CSTER 1175 1085950 1086225 − histone-like DNA-  95% 4.00E−40  72% DNA-binding binding prot. protein HU 1 CSTER 1182 1091629 1092501 − Geranylgeranyl  89% 5.00E−58  44% Farnesyl diphosphate pyrophosphate synthase synthase ispa yqid CSTER 1188 1095764 1096462 − DNA replication  85% 1.00E−07  22% DNA replication prot. DnaD protein DnaD CSTER 1193 1101272 1102201 − ribonuclease Z  99% 2.00E−105 50% Ribonuclease Z rnz CSTER 1197 1105450 1106877 − cell division prot.  88% 2.00E−57  38% Rod shape-determining protein RodA CSTER 1230 1131390 1132742 − Phosphoglucosamine 100% 0.00E+00  63% Phosphoglucosamine mutase mutase ybbt glnM CSTER 1248 1154457 1156616 + ribonucleotide-diphosphate  98% 0.00E+00  47% Ribonucleoside-diphosphate reductase, alpha subunit reductase subunit alpha nrde CSTER 1249 1156775 1157737 + ribonucleotide-diphosphate  97% 8.00E−98  49% Ribonucleoside-diphosphate reductase, beta subunit reductase subunit beta nrdf CSTER 1256 1161831 1164284 − DNA gyrase, A subunit  98% 0.00E+00  62% DNA gyrase subunit A CSTER 1267 1174041 1176449 − phenylalanyl-tRNA  99% 0.00E+00  47% synthetase, beta subunit CSTER 1270 1177285 1178328 − Phenylalanyl-tRNA  98% 3.00E−161 62% synthetase alpha subunit CSTER 1271 1178950 1182483 − chromosome segregation  99% 0.00E+00  37% Chromosome partition ATPase, SMC prot. protein Smc CSTER 1272 1182486 1183175 − ribonuclease III  89% 4.00E−68  47% Ribonuclease 3 CSTER 1273 1183332 1184267 − Dihydrodipicolinate  93% 5.00E−88  47% 4-hydroxy- synthase tetrahydrodipicolinate synthase dapA CSTER 1274 1184605 1185681 − Aspartate-semialdehyde  99% 1.00E−143 58% Aspartate-semialdehyde dehydrogenase dehydrogenase asd CSTER 1382 1293065 1294063 − Thioredoxin reductase  97% 7.00E−113 50% Ferredoxin--NADP reductase 2 yumc CSTER 1383 1294065 1294784 − tRNA (guanine-N(1)-)- 100% 6.00E−87  56% tRNA (guanine-N(1)-)- methyltransferase methyltransferase CSTER 1395 1303326 1304261 − methionyl-tRNA  96% 5.00E−98  49% formyltransferase CSTER 1396 1304279 1306675 − primosome assembly  99% 0.00E+00  48% Primosomal protein PriA protein N PriA CSTER 1398 1307153 1307782 − Guanylate kinase  98% 5.00E−87  59% Guanylate kinase gmk CSTER 1399 1308015 1309406 − cell division prot. FtsY  97% 8.00E−121 55% Signal recognition particle receptor FtsY CSTER 1422 1330503 1331339 − inorganic polyphosphate/ 100% 5.00E−78  44% NAD kinase 1 ppnk ATP-NAD kinase CSTER 1425 1333019 1333990 + ribose-phosphate 100% 4.00E−113 54% Ribose-phosphate pyrophosphokinase pyrophosphokinase prs CSTER 1426 1333994 1335106 + put. cysteine desulfurase  98% 2.00E−115 47% Putative cysteine desulfurase lscS CSTER 1448 1355769 1356878 − RNA polymerase  93% 6.00E−167 70% RNA polymerase sigma factor RpoD sigma factor SigA CSTER 1449 1356882 1358693 − DNA primase  68% 9.00E−86  37% DNA primase DnaG CSTER 1451 1359076 1359252 − 30S ribosomal prot. S21  98% 3.00E−29  89% CSTER 1464 1371306 1372619 − GTPase ObgE 100% 0.00E+00  67% GTPase ObgE CSTER 1480 1387053 1389005 − DNA gyrase subunit B 100% 0.00E+00  68% DNA gyrase subunit B CSTER 1497 1401241 1402143 − UDP-N-  98% 1.00E−66  40% UDP-N- acetylenolpyruvoylglucosamine acetylenolpyruvoylglucosamine reductase reductase murB CSTER 1506 1409996 1410268 − 30S ribosomal prot. S16 100% 5.00E−42  67% CSTER 1512 1415065 1416078 − put. lipid kinase  95% 1.00E−96  51% Diacylglycerol kinase dagK CSTER 1513 1416088 1418034 − NAD-dependent DNA ligase  97% 0.00E+00  55% DNA ligase LigA CSTER 1516 1419659 1420519 − methionine aminopeptidase  99% 6.00E−56  37% CSTER 1519 1422447 1423709 − UDP-N-acetylglucosamine  96% 6.00E−125 46% UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1-carboxyvinyltransferase 1 muraa CSTER 1522 1426828 1427583 − 1-acyl-sn-glycerol-3-  92% 1.00E−29  32% 1-acyl-sn-glycerol- phosphate acyltransferase 3-phosphate acyltransferase plsC CSTER 1534 1439747 1441120 − UDP-N-acetylmuramoyl-  98% 2.00E−98  38% UDP-N-acetylmuramoyl- tripeptide--D-alanyl- tripeptide--D-alanyl- D-alanine ligase D-alanine ligase murF CSTER 1544 1447537 1448583 − D-alanyl-alanine  98% 2.00E−95  42% D-alanine--D- synthetase A alanine ligase ddl CSTER 1583 1483475 1484107 − nicotinic acid  98% 2.00E−62  44% Nicotinate-nucleotide mononucleotide adenylyltransferase nadd adenylyltransferase CSTER 1584 1484211 1484528 − put. RNA-  95% 1.00E−24  50% Probable RNA- binding prot. binding protein Yqel CSTER 1585 1484767 1485885 − GTP-binding 100% 6.00E−163 59% Uncharacterized prot. YqeH protein YqeH CSTER 1590 1488021 1489463 − aspartyl/glutamyl-tRNA  99% 0.00E+00  63% amidotransferase subunit B CSTER 1591 1489463 1490929 − aspartyl/glutamyl-tRNA  99% 0.00E+00  59% amidotransferase subunit A CSTER 1592 1490929 1491231 − aspartyl/glutamyl-tRNA  97% 1.00E−18  41% amidotransferase subunit C CSTER 1615 1511378 1512298 − Thioredoxin reductase  95% 3.00E−126 58% Thioredoxin reductase trxb CSTER 1665 1554189 1555211 − phospho-N-  92% 1.00E−66  41% Phospho-N- acetylmuramoyl- acetylmuramoyl- pentapeptide- pentapeptide- transferase transferase mray CSTER 1666 1555213 1557480 − put. penicillin-binding  90% 9.00E−88  32% Penicillin-binding protein 2X protein 2B CSTER 1667 1557484 1557804 − cell division prot. FtsL CSTER 1701 1591284 1592387 − Alanine racemase  93% 1.00E−98  43% Alanine racemase 1 alr CSTER 1702 1592408 1592767 − put. 4′-  97% 6.00E−29  41% Holo-[acyl- phosphopantetheinyl carrier-protein] transferase synthase CSTER 1705 1594955 1597504 − preprotein translocase 100% 0.00E+00  55% Protein translocase subunit SecA subunit SecA CSTER 1726 1616337 1616576 − 30S ribosomal prot. S18 100% 5.00E−32  65% CSTER 1727 1616618 1617136 − single-strand DNA-  93% 1.00E−41  56% Single-stranded DNA- binding prot. binding protein B CSTER 1728 1617148 1617438 − 30S ribosomal prot. S6  96% 4.00E−40  61% CSTER 1745 1633808 1634821 − put. O-sialoglycoprotein  97% 6.00E−130 55% tRNA N6-adenosine endopeptidase threonylcarbamoyltransferase tsad CSTER 1747 1635236 1635922 − put. glycoprotein 100% 6.00E−44  38% tRNA endopeptidase threonylcarbamoyladenosine biosynthesis protein TsaB CSTER 1749 1636421 1638103 + mRNA degradation  99% 0.00E+00  62% Ribonuclease ribonucleases J1/J2 J1 yqkc CSTER 1755 1642501 1643700 − phosphoglycerate kinase 100% 2.00E−124 50% Phosphoglycerate kinase pgk CSTER 1762 1648240 1650321 − translation elongation 100% 0.00E+00  77% factor G CSTER 1763 1650542 1651012 − 30S ribosomal prot. S7 100% 1.00E−86  75% CSTER 1764 1651031 1651444 − 30S ribosomal prot. S12  98% 3.00E−80  86% CSTER 1770 1656078 1656950 − ribosome-associated  99% 5.00E−105 51% Putative GTPase ribosome biogenesis GTPase RsgA CSTER 1776 1660099 1660413 − put. thioredoxin  92% 1.00E−37  61% Thioredoxin trxa CSTER 1787 1670058 1670192 − 505 ribosomal prot. L34 100% 1.00E−15  70% CSTER 1790 1673060 1673395 − ribonuclease P  95% 1.00E−31  47% Ribonuclease P protein component CSTER 1793 1677296 1678750 − Glutamyl-tRNA 100% 0.00E+00  55% synthetases CSTER 1797 1681106 1681795 − 505 ribosomal prot. L1  98% 4.00E−99  65% 505 ribosomal protein L1 CSTER 1809 1690036 1691058 + Glycerol-3-phosphate  94% 4.00E−122 53% Glycerol-3-phosphate dehydrogenase dehydrogenase [NAD(P)+] gspA CSTER 1813 1693298 1694431 − Metal-dependent  95% 6.00E−120 47% N-acetyldiaminopimelate amidase/aminoacylase/ deacetylase ykur carboxypeptidase CSTER 1814 1694510 1695208 − put. 2,3,4,5-  98% 4.00E−86  60% 2,3,4,5-tetrahydropyridine- tetrahydropyridine- 2,6-dicarboxylate 2-carboxylate N-acetyltransferase N-succinyltransferase dapH CSTER 1821 1699209 1699601 − single-strand  93% 1.00E−25  40% Single-stranded DNA- binding prot. binding protein B CSTER 1844 1713286 1716924 − DNA-directed RNA  97% 0.00E+00  68% DNA-directed RNA polymerase subunit beta′ polymerase subunit beta CSTER 1845 1717025 1720606 − DNA-directed RNA  98% 0.00E+00  71% DNA-directed RNA polymerase subunit beta polymerase subunit beta′ CSTER 1847 1723493 1724749 + Tyrosyl-tRNA synthetase  99% 0.00E+00  58% CSTER 1876 1751169 1752050 − fructose- 100% 4.00E−83  45% Probable bisphosphate aldolase fructose-bisphosphate aldolase fbaa CSTER 1880 1755102 1755488 − 50S ribosomal prot. L17 100% 2.00E−62  73% CSTER 1881 1755506 1756444 − DNA-directed RNA  99% 7.00E−139 62% DNA-directed RNA polymerase alpha subunit polymerase subunit alpha CSTER 1882 1756493 1756876 − 30S ribosomal prot. S11  93% 7.00E−69  87% CSTER 1883 1756904 1757269 − 30S ribosomal prot. S13 100% 2.00E−58  73% CSTER 1884 1757290 1757403 − 50S ribosomal prot. L36 100% 4.00E−16  84% CSTER 1885 1757429 1757647 − Translation initiation 100% 1.00E−38  78% factor 1 (IF-1) CSTER 1886 1757765 1758421 − Adenylate kinase  99% 3.00E−89  59% Adenylate kinase adk CSTER 1887 1758553 1759848 − preprot. translocase  99% 4.00E−140 49% Protein translocase subunit SecY subunit SecY CSTER 1888 1759865 1760305 − 50S ribosomal prot. L15 100% 1.00E−70  72% CSTER 1889 1760433 1760615 − 50S ribosomal prot. L30  98% 3.00E−20  62% CSTER 1890 1760630 1761124 − 30S ribosomal prot. S5  93% 8.00E−70  76% CSTER 1891 1761143 1761499 − 50S ribosomal prot. L18 100% 4.00E−55  73% CSTER 1892 1761589 1762125 − 50S ribosomal prot. L6 100% 3.00E−69  60% 50S ribosomal protein L6 CSTER 1893 1762252 1762650 − 30S ribosomal prot. S8 100% 1.00E−73  77% CSTER 1894 1762773 1762958 − 30S ribosomal prot. S14 100% 1.00E−31  77% CSTER 1895 1762976 1763518 − 505 ribosomal prot. L5  99% 3.00E−100 77% CSTER 1896 1763545 1763850 − 505 ribosomal prot. L24  99% 7.00E−38  64% CSTER 1897 1763931 1764299 − 505 ribosomal prot. L14 100% 5.00E−74  87% CSTER 1898 1764324 1764584 − 30S ribosomal prot. S17  97% 4.00E−46  84% CSTER 1899 1764612 1764818 − 50S ribosomal prot. L29  78% 1.00E−14  58% CSTER 1900 1764828 1765241 − 50S ribosomal prot. L16  93% 1.00E−76  83% CSTER 1901 1765245 1765898 − 30S ribosomal prot. S3 100% 1.00E−119 75% CSTER 1902 1765911 1766255 − 50S ribosomal prot. L22  96% 7.00E−49  64% CSTER 1903 1766271 1766549 − 30S ribosomal prot. S19 100% 2.00E−54  83% CSTER 1904 1766643 1767476 − 50S ribosomal prot. L2 100% 5.00E−159 76% 50S ribosomal protein L2 CSTER 1905 1767494 1767790 − 50S ribosomal prot. L23  94% 2.00E−31  60% CSTER 1906 1767790 1768413 − 50S ribosomal prot. L4 100% 9.00E−92  60% 50S ribosomal protein L4 CSTER 1907 1768438 1769064 − 50S ribosomal prot. L3  99% 4.00E−115 75% 50S ribosomal protein L3 CSTER 1908 1769181 1769489 − 30S ribosomal prot. S10 100% 1.00E−58  78% CSTER 1936 1795296 1795484 + 50S ribosomal prot. L28 100% 7.00E−26  69% CSTER 1948 1805428 1807179 − Aspartyl-tRNA synthetase  98% 0.00E+00  57% CSTER 1950 1807719 1808999 − Histidyl-tRNA synthetase  99% 1.00E−140 49% CSTER 1953 1810651 1810833 + 50S ribosomal prot. L32  91% 1.00E−10  48% CSTER 1954 1810849 1810998 + 50S ribosomal prot. L33 100% 1.00E−14  55% CSTER 1973 1823718 1824329 − 30S ribosomal prot. S4 100% 1.00E−95  69% CSTER 1975 1824852 1826213 − replicative  95% 8.00E−176 56% Replicative DNA DNA helicase helicase DnaC CSTER 1976 1826257 1826715 − 50S ribosomal prot. L9 100% 2.00E−39  55% CSTER 1979 1830931 1832052 − tRNA (5-  98% 9.00E−177 70% tRNA-specific methylaminomethyl-2- 2-thiouridylase thiouridylate)- MnmA methyltransferase CSTER 1986 1838183 1838725 − Phosphatidylglycerophosphate  93% 2.00E−45  52% CDP-diacylglycerol-- synthase glycerol-3-phosphate 3- phosphatidyltransferase pgsA CSTER 1992 1843910 1845391 − inositol-5-monophosphate  99% 0.00E+00  68% Inosine-5′- dehydrogenase monophosphate dehydrogenase guab CSTER 1993 1845568 1846590 − Tryptophanyl-tRNA  98% 8.00E−42  35% synthetase II

TABLE 5 List of differentially expressed genes identified in deletion strain GEI4. Regulator- Operon Putative pathway/function effector Gene log₂ change p-value STER_0390_ Cysteine Cmbr/ STER_0390 −1.1  2.7E−23 STER-0393 metabolism Homr/ STER_0391 −1.3  2.2E−22 Mtar STER_0392 −1.4  1.2E−32 STER_0393 −1.2  2.8E−16 STER_1016- Maltodextrin STER_1016 −1.0 0 STER_1017 metabolism STER_1017 −0.8 7.50E−38 STER_1548- Aromatic amino T-box STER_1648 −1.3  2.3E−37 STER_1556 acid biosynthesis RNA STER_1549 −1.0  1.5E−25 (Trp) STER_1560 −1.3  7.9E−38 STER_1561 −1.3  1.2E−38 STER_1562 −1.3 0 STER_1563 −1.4 0 STER_1564 −1.3 0 STER_1566 −1.e  7.6E−73 STER_1960- Membrane proteins STER_1960 −0.9 0 STER_1963 STER_1961 −1.0 0 STER_1962 −1.0  8.3E−317 STER_1963 −1.1  3.2E−955 STER_0049- Purine biosynthesis PurR STER_0049 1.2  6.6E−34 STER_0054 STER_0060 1.1  1.4E−29 STER_0061 1.1 0 STER_0062 1.1 0 STER_0063 1.1 0 STER_0064 1.1   6.E−40 STER_0699- Ethanolamine STER_0699 1.6 0 STER_0701 metabolism STER_0700 2.1  9.6E−200 STER_0701 2.2  7.8E−329 STER_1020- Twin arginine TatA STER_1020 1.3  6.3E−14 STER_1024 translocase STER_1021 1.3  8.8E−12 STER_1022 1.4  3.3E−12 STER_1023 1.0  9.6E−6 STER_1024 0.9 0.0022 STER_1025- Iron homeostesis PerR STER_1026 1.1  1.9E−09 STER_1028 STER_1020 0.9  2.5E−6 STER_1027 1.2    3E−12 STER_1028 1.2  1.6E−17 STER_1405- ABC Peptide Cody STER_1405 1.8  9.6E−90 STER_1409 Transport STER_1406 1.6 0 STER_1407 1.5  3.7E−69 STER_1408 1.6 0 STER_1409 1.4  4.2E−64 STER_1821- Stress STER_1821 2.0 0 STER_1823 STER_1822 2.2  6.4E−98 STER_1823 2.0 0

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The foregoing is illustrative of the present invention and is not to be construed as limiting thereof. The invention is defined by the following claims, with equivalents of the claims to be included therein. 

1-30. (canceled)
 31. A method of selectively killing a specific bacterial subset within a mixed population of bacterial cells, the method comprising: introducing into the mixed population of bacterial cells (a) a heterologous nucleic acid construct comprising a CRISPR array that is functional with an endogenous CRISPR-Cas system present in the specific bacterial subset, and/or (b) a CRISPR array and a CRISPR-Cas system, wherein the CRISPR array and the CRISPR-Cas system of (b) are introduced on the same or in separate heterologous nucleic acid constructs, in any combination, wherein the CRISPR array of (a) and (b) comprises (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, and the spacer of the repeat-spacer-repeat sequence or the repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in a conserved genetic sequence of the specific bacterial subset that is distinct from other bacterial cells in the mixed population, the target region having at least 10 consecutive nucleotides adjacent to a protospacer-adjacent motif (PAM) recognized by the endogenous CRISPR-Cas system of (a) or the CRISPR-Cas system of (b), thereby selectively killing the specific bacterial subset that comprises the target region.
 32. The method of claim 31, wherein the endogenous CRISPR-Cas system of (a) is: (i) a Type I CRISPR-Cas system and the CRISPR array is a Type I CRISPR array, (ii) a Type II CRISPR-Cas system and the CRISPR array is a Type II CRISPR array, (iii) a Type III CRISPR-Cas system and the CRISPR array is a Type III CRISPR array, (iv) a Type IV CRISPR-Cas system and the CRISPR array is a Type IV CRISPR array, or (v) a Type V CRISPR-Cas system and the CRISPR array is a Type V CRISPR array.
 33. The method of claim 31, wherein the CRISPR-Cas system of (b) is: (i) a Type I CRISPR-Cas system and the CRISPR array is a Type I CRISPR array, (ii) a Type II CRISPR-Cas system and the CRISPR array is a Type II CRISPR array, (iii) a Type III CRISPR-Cas system and the CRISPR array is a Type III CRISPR array, (iv) a Type IV CRISPR-Cas system and the CRISPR array is a Type IV CRISPR array, or (v) a Type V CRISPR-Cas system and the CRISPR array is a Type V CRISPR array.
 34. The method of claim 33, wherein (i) the Type I CRISPR-Cas system of (b) comprises (A) at least one Type I Cascade polypeptide and (B) a Cas3 polypeptide, or a Cas3′ polypeptide and a Cas3″ polypeptide, and/or one or more heterologous nucleic acid constructs encoding (A) and/or (B); (ii) the Type II CRISPR-Cas system comprises a Cas9 polypeptide, and/or a nucleic acid construct encoding the Cas9 polypeptide, optionally wherein the Type II CRISPR-Cas system further comprises a tracrRNA; (iii) the Type III CRISPR-Cas system comprises at least one Csm complex polypeptide or at least one Cmr complex polypeptide, and/or one or more heterologous nucleic acid constructs encoding the at least one Csm complex polypeptide and/or the at least one Cmr complex polypeptide, and optionally a Cas6 polypeptide or a heterologous nucleic acid construct encoding the Cas6 polypeptide; (iv) the Type IV CRISPR-Cas system comprises at least one of a Csf4 (dinG) polypeptide, a Csf1 polypeptide, a Csf2 (Cas7) polypeptide and/or a Csf3 (Cas5) polypeptide, and/or one or more heterologous nucleic acid constructs encoding the at least one Csf4 polypeptide, Csf1 polypeptide, Csf2 polypeptide and/or CSf3 polypeptide; and (v) the Type V CRISPR-Cas system comprises a Cpf1 polypeptide, and/or a heterologous nucleic acid construct encoding the same.
 35. The method of claim 32, wherein the repeat-spacer-repeat sequence or the at least one repeat-spacer sequence of: (a) the Type I CRISPR array comprises a repeat that is identical to a repeat from a wild-type Type I CRISPR array, (b) the Type II CRISPR array comprises a repeat that is identical to a repeat from a wild type Type II CRISPR array, (c) the Type III CRISPR array comprises a repeat that is identical to a repeat from a wild type Type III CRISPR array, (d) the Type IV CRISPR array comprises a repeat that is identical to a repeat from a wild type Type IV CRISPR array, or (e) the Type V CRISPR array comprises a repeat that is identical to a repeat from a wild type Type V CRISPR array.
 36. The method of claim 33, wherein the repeat-spacer-repeat sequence or the at least one repeat-spacer sequence of: (a) the Type I CRISPR array comprises a repeat that is identical to a repeat from a wild-type Type I CRISPR array, (b) the Type II CRISPR array comprises a repeat that is identical to a repeat from a wild type Type II CRISPR array, (c) the Type III CRISPR array comprises a repeat that is identical to a repeat from a wild type Type III CRISPR array, (d) the Type IV CRISPR array comprises a repeat that is identical to a repeat from a wild type Type IV CRISPR array, or (e) the Type V CRISPR array comprises a repeat that is identical to a repeat from a wild type Type V CRISPR array.
 37. The method of claim 31, wherein at least one or more bacterial cells of the mixed population does not comprise the target sequence and, therefore, the at least one or more bacterial cells are not killed upon introduction of the CRISPR array.
 38. The method of claim 31, wherein the spacer of the repeat-spacer-repeat sequence or the at least one repeat-spacer sequence comprises a nucleotide sequence that is 100% complementary to the target sequence.
 39. The method of claim 31, wherein the target sequence is selected from a gene, open reading frame or a putative open reading frame or an intergenic region, optionally wherein the target sequence is within an essential gene and/or a non-essential gene.
 40. The method of claim 31, further comprising introducing into the mixed population of bacterial cells a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid.
 41. The method of claim 31, wherein the heterologous nucleic acid construct is comprised in a phage.
 42. A method of identifying in a population of bacterial cells at least one isolate that does not comprise in its genome a conserved target region that is present in the genome of one or more bacterial cells in the population, comprising: introducing into the population of bacterial cells (a) a heterologous nucleic acid construct comprising a CRISPR array that is functional with an endogenous CRISPR-Cas system present in the specific bacterial subset, and/or (b) a CRISPR array and a CRISPR-Cas system, wherein the CRISPR array and the CRISPR-Cas system of (b) are introduced on the same or in separate heterologous nucleic acid constructs, in any combination, wherein the CRISPR array comprises (5′ to 3′) a repeat-spacer-repeat sequence or at least one repeat-spacer sequence, and the spacer of the repeat-spacer-repeat sequence or the repeat-spacer sequence comprises a nucleotide sequence that is substantially complementary to a target region in a conserved genetic sequence of the specific bacterial subset that is distinct from other bacterial cells in the mixed population, the target region having at least 10 consecutive nucleotides adjacent to a protospacer-adjacent motif (PAM) recognized by the endogenous CRISPR-Cas system of (a) or the CRISPR-Cas system of (b); detecting the presence or absence of the conserved target region in the genome of at least one isolate from the population of bacterial cells, and identifying at least one isolate that does not comprise the conserved target region in its genome.
 43. The method of claim 42, wherein the endogenous CRISPR-Cas system of (a) is: (i) a Type I CRISPR-Cas system and the CRISPR array is a Type I CRISPR array, (ii) a Type II CRISPR-Cas system and the CRISPR array is a Type II CRISPR array, (iii) a Type III CRISPR-Cas system and the CRISPR array is a Type III CRISPR array, (iv) a Type IV CRISPR-Cas system and the CRISPR array is a Type IV CRISPR array, or (v) a Type V CRISPR-Cas system and the CRISPR array is a Type V CRISPR array.
 44. The method of claim 42, wherein the CRISPR-Cas system of (b) is: (i) a Type I CRISPR-Cas system and the CRISPR array is a Type I CRISPR array, (ii) a Type II CRISPR-Cas system and the CRISPR array is a Type II CRISPR array, (iii) a Type III CRISPR-Cas system and the CRISPR array is a Type III CRISPR array, (iv) a Type IV CRISPR-Cas system and the CRISPR array is a Type IV CRISPR array, or (v) a Type V CRISPR-Cas system and the CRISPR array is a Type V CRISPR array.
 45. The method of claim 44, wherein (i) the Type I CRISPR-Cas system of (b) comprises (A) at least one Type I Cascade polypeptide and (B) a Cas3 polypeptide, or a Cas3′ polypeptide and a Cas3″ polypeptide, and/or one or more heterologous nucleic acid constructs encoding (A) and/or (B); (ii) the Type II CRISPR-Cas system comprises a Cas9 polypeptide, and/or a nucleic acid construct encoding the Cas9 polypeptide, optionally wherein the Type II CRISPR-Cas system further comprises a tracrRNA; (iii) the Type III CRISPR-Cas system comprises at least one Csm complex polypeptide or at least one Cmr complex polypeptide, and/or one or more heterologous nucleic acid constructs encoding the at least one Csm complex polypeptide and/or the at least one Cmr complex polypeptide, and optionally a Cas6 polypeptide or a heterologous nucleic acid construct encoding the Cas6 polypeptide; (iv) the Type IV CRISPR-Cas system comprises at least one of a Csf4 (dinG) polypeptide, a Csf1 polypeptide, a Csf2 (Cas7) polypeptide and/or a Csf3 (Cas5) polypeptide, and/or one or more heterologous nucleic acid constructs encoding the at least one Csf4 polypeptide, Csf1 polypeptide, Csf2 polypeptide and/or CSf3 polypeptide; and (v) the Type V CRISPR-Cas system comprises a Cpf1 polypeptide, and/or a heterologous nucleic acid construct encoding the same.
 46. The method of claim 43, wherein the repeat-spacer-repeat sequence or the at least one repeat-spacer sequence of: (a) the Type I CRISPR array comprises a repeat that is identical to a repeat from a wild-type Type I CRISPR array, (b) the Type II CRISPR array comprises a repeat that is identical to a repeat from a wild type Type II CRISPR array, (c) the Type III CRISPR array comprises a repeat that is identical to a repeat from a wild type Type III CRISPR array, (d) the Type IV CRISPR array comprises a repeat that is identical to a repeat from a wild type Type IV CRISPR array, or (e) the Type V CRISPR array comprises a repeat that is identical to a repeat from a wild type Type V CRISPR array.
 47. The method of claim 44, wherein the repeat-spacer-repeat sequence or the at least one repeat-spacer sequence of: (a) the Type I CRISPR array comprises a repeat that is identical to a repeat from a wild-type Type I CRISPR array, (b) the Type II CRISPR array comprises a repeat that is identical to a repeat from a wild type Type II CRISPR array, (c) the Type III CRISPR array comprises a repeat that is identical to a repeat from a wild type Type III CRISPR array, (d) the Type IV CRISPR array comprises a repeat that is identical to a repeat from a wild type Type IV CRISPR array, or (e) the Type V CRISPR array comprises a repeat that is identical to a repeat from a wild type Type V CRISPR array.
 48. The method of claim 42, wherein at least one or more bacterial cells of the mixed population does not comprise the target sequence and, therefore, the at least one or more bacterial cells are not killed upon introduction of the CRISPR array.
 49. The method of claim 42, wherein the spacer of the repeat-spacer-repeat sequence or the at least one repeat-spacer sequence comprises a nucleotide sequence that is 100% complementary to the target sequence.
 50. The method of claim 42, wherein the target sequence is selected from a gene, open reading frame or a putative open reading frame or an intergenic region, optionally wherein the target sequence is within an essential gene and/or a non-essential gene.
 51. The method of claim 42, further comprising introducing into the mixed population of bacterial cells a heterologous nucleic acid construct comprising a trans-encoded CRISPR (tracr) nucleic acid.
 52. The method of claim 42, wherein the heterologous nucleic acid construct is comprised in a phage. 